- IPT - lists.gbif.org

IPT XML metadata
by torsten dikow 19 Aug '11

19 Aug '11

Hi IPT users, I have recently uploaded occurrence data from a published article to the Pensoft IPT instance. In order to set-up an XML meta file, I used the Darwin Core Archive assistant and exported that XML file thinking that I would need it when I upload the resource to the IPT. But when I tried to map my columns on the IPT, I couldn't just upload that XML file and needed to select each column from a drop-down menu. This seems to me to be double work and I would rather like to use the XML meta file generated by the Darwin Core Archive assistant. This XML meta file had the columns arranged in a way so that they correspond to the exported occurrence data from my FileMaker Pro database. Is there any way I can use the XML meta file for mapping columns? Thanks, Torsten Dikow

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Re: [IPT] IPT Digest, Vol 30, Issue 5
by Stewart, Aimee Marian 17 Aug '11

17 Aug '11

Sent from 785-331-8952. "ipt-request(a)lists.gbif.org" <ipt-request(a)lists.gbif.org> wrote: Send IPT mailing list submissions to ipt(a)lists.gbif.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gbif.org/mailman/listinfo/ipt or, via email, send a message with subject or body 'help' to ipt-request(a)lists.gbif.org You can reach the person managing the list at ipt-owner(a)lists.gbif.org When replying, please edit your Subject line so it is more specific than "Re: Contents of IPT digest..." Today's Topics: 1. Re: GBIF Case 1773: UTF8 (Mickael Graf) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Aug 2011 14:38:53 +0200 From: Mickael Graf <Mickael.Graf(a)nrm.se> Subject: Re: [IPT] GBIF Case 1773: UTF8 To: "Burke Chih-Jen Ko (GBIF)" <bko(a)gbif.org> Cc: GBIF IPT mailing list <ipt(a)lists.gbif.org>, Johan Dunfalk <Johan.Dunfalk(a)nrm.se>, GBIF Helpdesk <helpdesk(a)gbif.org> Message-ID: <9F4FCAEFF4CBCB4CA1AF9E8BDABF4B8FA3629854B0@saruman> Content-Type: text/plain; charset="iso-8859-1" > 1. Did you use mysqldump to create the script that you sent me earlier? Yes, for the table definition and the data. The script for the view is hand written. > 2. From the script, I can see the database stores data in UTF-8, is it correct? Unfortunately no. Default settings for the server are latin1 so is the database. The data itself is (well, shoud be...) utf8 and the table definition has utf8 as character set. >3. Since the character in the dump sql is already broken, could you try, if you temporarily change the connection charset to utf-8, does the same dump contains the correct character for accented letters? Or please try --default-character-set=latin1 as one of your dump option. I just did a dump with --default-character-set=latin1 and I can read the accented letters in less,emacs and firefox (where I need to specify it's utf8). >4. Since all charset settings on your side appear to be latin1, are all databases hosted on the mysql server using UTF8 as the encoding? Including the one serves TapirLink? Most of my databases use latin1, but I have two of them created using utf8. But for all of them the accented letters are correctly displayed with TapirLink. Cheers, Micka?l I am trying to reproduce your environment here. Cheers, Burke On Aug 16, 2011, at 9:26 AM, Mickael Graf wrote: > Hi Burke, > > I tried both UTF-8, Latin1 and Windows 1252, but the result looks always the same. It looks like this setting has no influence on the final result, at least here. > > /Micka?l > > ________________________________________ > From: Burke Chih-Jen Ko (GBIF) [bko(a)gbif.org] > Sent: Monday, August 15, 2011 4:24 PM > To: Mickael Graf > Cc: Johan Dunfalk; GBIF IPT mailing list > Subject: Re: GBIF Case 1773: UTF8 > > Hi Micha?l, > > Have you tried using Latin 1 as the character encoding in the source data editing page of IPT? > > Burke > > On Aug 15, 2011, at 3:19 PM, Mickael Graf wrote: > >> Hi Burke, >> >> Changing my.cnf breaks everything. So I reversed back. I need to study how to correctly migrate my data to a complete utf8 system. >> MySQL still comes with latin1 as default (I just checked on my Ubuntu 11.04!) >> >> How can I test Tim's suggestion? >> >> Cheers, >> Micka?l >> >> ________________________________________ >> From: Burke Chih-Jen Ko (GBIF) [bko(a)gbif.org] >> Sent: Friday, August 12, 2011 4:30 PM >> To: Mickael Graf >> Cc: Johan Dunfalk; GBIF IPT mailing list >> Subject: Re: GBIF Case 1773: UTF8 >> >> Hi Micka?l, >> >> I can see from your script that the database is created using UTF-8, but it could be the connection characterset that interprets the UTF-8 information as iso-8859-1. Force opening a UTF-8 text file with N?rke using latin1 charset indeed render the text as N??rke. >> >> In the [mysqld] section of /etc/my.cnf, you can instruct the server to start with preferred characterset and collation: >> >> character_set_server=utf8 >> default-character-set=utf8 >> character_set_client=utf8 >> collation_server=utf8_general_ci >> skip-character-set-client-handshake >> >> The last line force the connection charset as the one specified for the server. >> >> So I suggest some steps: >> 1. Add lines above to your my.cnf >> 2. Restart the mysql, >> 3. First see if things still looks the same on TapirLink. >> 4. Try export the same sample script you gave us earlier, if the n?rke shows as it should be, then it should be fine on IPT. >> >> Let me know if this setting works. >> >> But if this change breaks TapirLink and others, you'll need to decide to configure others all or, see if Tim's suggestion works. (jdbc:mysql://localhost:3306/specimen_collections?autoReconnect=true&useUnicode=true&characterEncoding=UTF8&characterSetResults=UTF8) >> >> Cheers, >> >> Burke >> > > ------------------------------ _______________________________________________ IPT mailing list IPT(a)lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt End of IPT Digest, Vol 30, Issue 5 **********************************

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FW: UTF8
by GBIF Helpdesk 11 Aug '11

11 Aug '11

-----Original Message----- From: Mickael Graf [mailto:Mickael.Graf@nrm.se] Sent: 10 August 2011 16:25 To: helpdesk(a)gbif.org Subject: UTF8 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

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Re: [IPT] Request to be added as commiter
by Tim Robertson (GBIF) 12 Jul '11

12 Jul '11

Dear Shiraaz, Thank you for your interest in the IPT and willingness to contribute. It would be fantastic to have external contributions. Like many open source projects, the way in which we would like to operate is to have contributors submit a patch, which would be reviewed by a committer. Following some successful patches, the contributer would be welcomed as a committer. As a fairly immature project, we don't yet have a large pool of contributers, so it is an exciting time to get involved early. The IPT is very lacking in unit test coverage as you mention and is highlighted in sonar[1]. Increasing the unit test coverage would be a good way to really help improve the project, and learn the code structure. We have just set up a review system[2] as well, which allows easier review of patches. I would recommend offering a patch there and we can review it. Does this help to get started? Many thanks again for your interest, Tim [1] http://sonar.gbif.org/dashboard/index/1498 [2] http://reviews.gbif.org On Jul 12, 2011, at 2:14 PM, Shiraaz Moollatjie wrote: > Hi, > > I am totally new to the open source development world and I noticed > the gbif-providertoolkit which seems interesting to me. Since I am > totally new to this (and probably breaking all sorts of etiquette > involved, my apologies if I am :) ) I was wondering what I can do to > get started on the project? My guess is that since I did not prove > myself as a developer yet, I was hoping to maybe add some unit tests > or do some documentation tasks for the project? > > My apologies again if I am taking the wrong approach here. Hopefully > you will give me some direction :). > > Kindest Regards, > Shiraaz

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Invitation to collaborate in the translation of the IPT user interface into Spanish
by Alberto González-Talaván (GBIF) 12 Jul '11

12 Jul '11

Dear friends of the IPT list, Please find below an invitation to collaborate in the translation of the IPT interface into Spanish. Cheers Alberto --------- Estimados amigos, Como muchos/as de ustedes saben, la nueva versión de la herramienta integrada de publicación de datos IPT (Integrated Publishing Toolkit) se publicó a principios de este año, y recientemente hemos celebrado un taller de formación en Copenhague donde 20 profesionales recibieron formación avanzada sobre la herramienta. Para hacer esta herramienta clave más accesible al público hispano hablante, sería muy útil disponer de la interfaz de usuario en Español. Uno de los desarrolladores de la herramienta en Colombia (Héctor Tobón) está interesado en comenzar este trabajo pero necesitaría algo de ayuda, sobre todo para traducir algunos términos más complejos, como los que se utilizan para describir los metadatos. Nos gustaría contar con su colaboración para realizar esta tarea. Por favor, si alguno/a de ustedes está interesado/a en participar en este pequeño proyecto, por favor contacte con nosotros a través de la red de idioma Español del Sitio de la Comunidad de GBIF (http://community.gbif.org/pg/groups/5947/red-de-idiomas-espaol/) o póngase en contacto con nosotros a través de la dirección training(a)gbif.org. ¡Gracias por adelantado! ---------- Alberto GONZÁLEZ TALAVÁN Senior Programme Officer for Training Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark email: <mailto:atalavan@gbif.org> atalavan(a)gbif.org web: http://www.gbif.org/ http://community.gbif.org/pg/profile/atalavan T: +45 35 32 14 83 F: +45 35 32 14 80

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Re: [IPT] IPT Digest, Vol 28, Issue 1
by Deependra Tandukar 02 Jun '11

02 Jun '11

HI, good news that new version is available? But what are the new in the IPT 2.02.? Best regards, Deependra -----Original Message----- From: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org] On Behalf Of ipt-request(a)lists.gbif.org Sent: Thursday, June 02, 2011 3:45 PM To: ipt(a)lists.gbif.org Subject: IPT Digest, Vol 28, Issue 1 Send IPT mailing list submissions to ipt(a)lists.gbif.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gbif.org/mailman/listinfo/ipt or, via email, send a message with subject or body 'help' to ipt-request(a)lists.gbif.org You can reach the person managing the list at ipt-owner(a)lists.gbif.org When replying, please edit your Subject line so it is more specific than "Re: Contents of IPT digest..." Today's Topics: 1. IPT 2.0.2 is available for download (Kyle Braak (GBIF)) 2. VASCAN metadata can now be downloaded as RTF (Peter Desmet) 3. Re: VASCAN metadata can now be downloaded as RTF (info(a)pensoft.net) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Jun 2011 14:42:20 +0200 From: "Kyle Braak (GBIF)" <kbraak(a)gbif.org> Subject: [IPT] IPT 2.0.2 is available for download To: ipt(a)lists.gbif.org Message-ID: <32FA1495-F355-49AA-8D46-025CDFD95102(a)gbif.org> Content-Type: text/plain; charset="us-ascii" Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.0.2) is now available for download from http://code.google.com/p/gbif-providertoolkit/. The IPT version 2.0.2 addresses 44 reported issues (http://tinyurl.com/gbif-ipt-202 ) from the previous version, and introduces a new Rich Text Format (RTF) export for dataset metadata. The RTF view of the metadata is designed to allow IPT users to submit data papers to journals such as Pensoft Zookeys, for peer review and publishing. More information on the data paper concept can be found on http://www.gbif.org/communications/news-and-events/showsingle/article/new-i… . Users of previous versions of the IPT may choose to update to benefit from this new functionality and bug fixing. Updating an IPT 2.0.x installation involves simply replacing the previous .war file with the latest edition, and reusing the existing data directory. Please remember that it is good practice to keep backups of the data directory, and we advise that you make a backup before performing an update. New users should follow the installation guidelines in the IPT documentation (http://code.google.com/p/gbif-providertoolkit/wiki/IPT2ManualNotes ). 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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Re: [IPT] [Fwd: RE: Training Sessions]
by Tim Robertson (GBIF) 02 Jun '11

02 Jun '11

Dear Raj, This error occurs because the machine the IPT is being installed on cannot make outgoing connections. I see the error is saying it cannot talk to the GBIF registry. The IPT administrator will need to investigate if there are ports closed or firewall restrictions stopping this from happening. On Linux the best way to ensure it is possible is to open a terminal and type "curl http://gbrds.gbif.org" There is also no need to install Geoserver for the IPT 2.0.x although there should not be an issue if you so wish to. I would suggest not to do so during training though as it might complicate things unnecessarily. Please can ensure all issues are sent to the to the IPT users list (ipt(a)lists.gbif.org ) which you will have to subscribe to if not already? There are more people on the list that can help diagnose potential issues, and quicker normally than I can alone. I hope this helps, Tim On Jun 2, 2011, at 3:08 PM, Raj K. Sood (GBIF) wrote: > Dear Tim, > > Kindly see the email below. Our partner at WII India has tried to > install > new version of IPT and encountered some problems as listed in their > email. > Screen shots of error msg are also attached herewith. > I also encountered error msg at point 5 and 6 of the following email. > > This is for your information and will keep you posted of any other > issues > that may come up while working with the new version of IPT. > > Thanks and take care, > > Best regards, > > > Raj Sood > GBIF Secretariat > E-mail: rsood(a)gbif.org > URL: www.gbif.org > ---------------------------- Original Message > ---------------------------- > Subject: RE: Training Sessions > From: "Dinesh Singh Pundir" <dspundir(a)wii.gov.in> > Date: Thu, June 2, 2011 9:32 am > To: "'Raj K. Sood \(GBIF\)'" <rsood(a)gbif.org> > Cc: vchavan(a)gbif.org > gautam(a)wii.gov.in > dspundir(a)gmail.com > -------------------------------------------------------------------------- > > Dear Mr. Raj, > > As suggested I downloaded the latest IPT version(ipt-2.0.2.war) and > tried to > install on the test machine. > > Following steps were followed > > 1. Installed java(jre-6u25-windows-i586), apache (apache- > tomcat-6.0.32) > and copied ipt.war and geoserver files in apache webapps directory. > 2. Run localhost:8080/ipt on the firefox browser. > 3. In IPT Setup-I (directory path as c:\iptdata was given) > 4. In IPT Setup-II (gave email, firstname, lastname, password etc. > under base url it automatically took path as http://DSPUNDIR:8080/ > ipt but it > showed error when I clicked on Save. > 5. Then I changed to base url to http://localhost:8080/ipt and clicked > on save. Then it directed to error screen (As shown in pdf attachment) > 6. In proxy URL I tried both by leaving it blank and next time I have > our Institute proxy server setting as http://192.168.201.254:8080 > Then it > directed to error screen (As shown in pdf attachment) > 7. After step 5 it showed error screen(pdf file) which I am attaching > you for your information and action. I am also sending you the log > screen in > pdf file. > > Kindly guide. > > Regards > > Dinesh Singh Pundir > > > > > > > <untitled-1.2><logs.pdf><IPT 2 Setup Error.pdf>

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VASCAN metadata can now be downloaded as RTF
by Peter Desmet 02 Jun '11

02 Jun '11

Hi all, I was intrigued by GBIF's announcement regarding publishing biodiversity data (http://bit.ly/m8hR6U), so I updated our IPT (http://ipt.canadensys.net) to 2.0.2 and republished our dataset (http://ipt.canadensys.net/resource.do?r=vascan). Users can now export the Database of Vascular Plants of Canada metadata as RTF (http://ipt.canadensys.net/rtf.do?r=vascan) and we could even submit this as a data paper to a Pensoft journal. Really cool and very easy! Good job IPT team! Peter PS: When I find some time, I'm going to dig a bit deeper in the RTF file and see how the EML->RTF transition went. -- Peter Desmet Biodiversity Informatics Manager / Directeur de l'informatique de la biodiversité Biodiversity Centre / Centre sur la biodiversité de l'Université de Montréal Canadensys - www.canadensys.net Institut de recherche en biologie végétale Université de Montréal 4101 rue Sherbrooke est Montréal, Québec, H1X2B2 Canada Télé / Phone: 514-343-6111 #82354 Télécopie / Fax: 514-343-2288 Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet

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IPT 2.0.2 is available for download
by Kyle Braak (GBIF) 01 Jun '11

01 Jun '11

Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.0.2) is now available for download from http://code.google.com/p/gbif-providertoolkit/. The IPT version 2.0.2 addresses 44 reported issues (http://tinyurl.com/gbif-ipt-202 ) from the previous version, and introduces a new Rich Text Format (RTF) export for dataset metadata. The RTF view of the metadata is designed to allow IPT users to submit data papers to journals such as Pensoft Zookeys, for peer review and publishing. More information on the data paper concept can be found on http://www.gbif.org/communications/news-and-events/showsingle/article/new-i… . Users of previous versions of the IPT may choose to update to benefit from this new functionality and bug fixing. Updating an IPT 2.0.x installation involves simply replacing the previous .war file with the latest edition, and reusing the existing data directory. Please remember that it is good practice to keep backups of the data directory, and we advise that you make a backup before performing an update. New users should follow the installation guidelines in the IPT documentation (http://code.google.com/p/gbif-providertoolkit/wiki/IPT2ManualNotes ). 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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How to configure IPT with Apache mod_proxy?
by janno jõgeva 31 May '11

31 May '11

Hello! I am quite new to this list so hello to everyone. Maybe I just missed something but here is my question. I am setting up an IPT node on our site. As IPT is not too much of a load it could run on a server that has other tasks as well. I have managed to set the IPT up and running via apache mod_proxy using jetty. I have daemonized it to a service on port 8080. The version I am using is ipt-2.0.2-SNAPSHOT-r3084. My ipt.properties is as follows: analytics.key= debug=false proxy= ipt.baseURL=http\://sitename.domain/ipt/ analytics.gbif=true defaultLocale=en and apache configured as: ... ProxyPass /ipt/ http://localhost:8080/ ProxyPassReverse /ipt/ http://localhost:8080/ ProxyPassReverseCookiePath /ipt / ProxyPreserveHost On ... Alias /ipt "/opt/ipt/webapp" <Directory "/opt/ipt/webapp"> ... My problem - the IPT runs fine - I can make changes for example in source data SQL configuration part. but whenever the application(IPT) has to call sitename.domain/ipt/admin/user.do it calls sitename.domain/admin/user.do instead and understandably fails. My question - is there a good documentation source for the ipt.properties file? If not then could you tell me what is the "proxy" configuration parameter for? Hope that the explanation is detailed enough. PS. IMHO a configuration file should have documentation for each and every parameter written inside the file. It would help a lot. Best wishes, Janno Jõgeva University of Tartu Natural History Museum

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