- IPT - lists.gbif.org

Fwd: Instalaci'on de ipt
by Ana Lorenzo 15 Jul '09

15 Jul '09

Perdón olvidé comprimir el archivo catalina.out Estimado Jose, > Le planteo mi problema y adjunto archivo catalina.out que en mi sistema est'a ubicado en la carpeta /usr/share/tomcat5/logs. > > Le doy detalles del entorno: > Sistema operativo: Ubuntu 8.04 > Apache 2.2.8 > Java Se SDK 1.4.2-19 Standard Edition > Tomcat 5.5.27 > > Instalaci'on de IPT: > segu'i las instrucciones del archivo GBIF_IPT_User_Manual_1.0.pdf > IPT qued'o instalado en la carpeta: usr/share/tomcat5/webapps/ipt > > El problema es: desde un browser, al dar http://localhost:8080/ipt da el > mensaje: > HTTP Status 404 - > ------------------------------ > > *type* Status report > > *message* > > *description* *The requested resource () is not available.* > ------------------------------ > Apache Tomcat/6.0.20 > Hice esta prueba: > cree esta la carpeta ana en: usr/share/tomcat5/webapps/ana, con un archivo > index.html > Cuando doy la URL http://localhost:8080/ana, funciona. > > Puede Ud. orientarme qu'e est'a pasando? > Gracias! y saludos. > > Ana Lorenzo > Laboratorio de Inform'atica > Instituto de Bot'anica Darwinion - IBODA > Argentina > >

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Fwd:Instalaci'on de ipt
by "Markus Döring (GBIF)" 15 Jul '09

15 Jul '09

[forwarding on behalf of Ana Lorenzo] [zipped catalina.out attachment as mailing list does not allow > 100kb] From: Ana Lorenzo <analorenzo2004(a)yahoo.com.ar> Date: July 14, 2009 15:43:33 GMT+02:00 To: ipt(a)lists.gbif.org Subject: Instalaci'on de ipt Estimado Jose, Le planteo mi problema y adjunto archivo catalina.out que en mi sistema est'a ubicado en la carpeta /usr/share/tomcat5/logs. Le doy detalles del entorno: Sistema operativo: Ubuntu 8.04 Apache 2.2.8 Java Se SDK 1.4.2-19 Standard Edition Tomcat 5.5.27 Instalaci'on de IPT: segu'i las instrucciones del archivo GBIF_IPT_User_Manual_1.0.pdf IPT qued'o instalado en la carpeta: usr/share/tomcat5/webapps/ipt El problema es: desde un browser, al dar http://localhost:8080/ipt da el mensaje: HTTP Status 404 - type Status report message description The requested resource () is not available. Apache Tomcat/6.0.20 Hice esta prueba: cree esta la carpeta ana en: usr/share/tomcat5/webapps/ana, con un archivo index.html Cuando doy la URL http://localhost:8080/ana, funciona. Puede Ud. orientarme qu'e est'a pasando? Gracias! y saludos. Ana Lorenzo Laboratorio de Inform'atica Instituto de Bot'anica Darwinion - IBODA Argentina

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IPT Short Installation Guide available in French
by Alberto González-Talaván (GBIF) 01 Jul '09

01 Jul '09

Dear friends, Michael Akbaraly from GBIF France has kindly produced a short installation guide in FRENCH for the GBIF IPT in MS Windows environments. The guide is available in PDF format in the download area of the IPT google code site: http://code.google.com/p/gbif-providertoolkit/downloads/list Thank you Michael for preparing this guide! Alberto ---------- Alberto GONZÁLEZ TALAVÁN Training Officer 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/ T: +45 35 32 14 83 F: +45 35 32 14 80

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How to define request with more that one filtering criteria in gbif density data service
by riihi tonttu 26 Jun '09

26 Jun '09

Hi, Sorry if this question is misplaced in this mailing list. If there is a mailing list that is more specifically focussed on the gbif webservices API, I’d be very grateful that you would give me the address of the list ( I’ve looked but haven’t been able to find one). I’d like to know how to define a request with more that one filtering criteria in the gbif density data service. For instance, the following request extracts a kml density file of all occurrences in Canada http://data.gbif.org/ws/rest/density/list?originisocountrycode=CA&format=kml However if I add the constraint that the occurrences come from the OBIS network: http://data.gbif.org/ws/rest/density/list?resourcenetworkkey=3&originisocou… only one constraint is taken into account (resourcenetworkkey), the originisocountrycode is disregarded. Is there any way of combining several filters in a density request? Thanks very much. saikari

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requesting a feature for posting elements written in regional language
by Burke Chih-Jen Ko 22 Jun '09

22 Jun '09

Hi Tim, Following what I briefly mentioned in the e-Biosphere, here I describe it to hopefully make it more comprehensive. Now we TaiBIF are doing data cleaning against our specimen data, one of the tasks is to separate information written in different languages. Take 'Locality' as an example, if an attribute is 'Taipei 台北', we move '台北' to a separate column named 'LocalityInChinese'. (Considering easiness for data providers, we decided to use 'InChinese' instead of 'zh_TW'.) Then you see several descriptive elements in Darwin Core could have their counterparts in Chinese, like Collector, Identifier, and many others. To be used by regional data providers, IPT will be even better if it can handle multiple languages. Actually we had thought about just keep all languages in one place, but I am afraid that it might create problems when information is exchanging worldwide. As I am aware that language issues could lead to further discussions of the standard, I, therefore, propose a neutral mechanism that users can add their own elements, so that once an element is created, it can automatically map to the column with the same name, when a SQL source is connected or a csv sheet is uploaded. There should also be statistics based on the new element, or users can decide they don't want it calculated. In this case, I would add 'LocalityInChinese' as the new element. Hope this make sense. Cheers, Chih-Jen(Burke)

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Re: [IPT] Adding an extension for germplasm to IPT
by Dag Terje Filip Endresen 27 May '09

27 May '09

Dear Eli, The instructions I received from Markus is actually already included here below as included in your email. I have also added the instructions from Tim, as also posted to the IPT mailing list. Basically what (I think) the IPT does is to contact the registry as defined in "ipt.properties". By default the GBIF registry in Copenhagen is defined here, but you may modify this to point to your own registry. I did not mimic the complete features of the registry - ONLY the list of extensions "extensions.json" to add the new draft germplasm extension I made. You may want to add your own thesaurus "thesauri.json" of controlled vocabulary or more features in the similar way. After loading my new extension to my IPT at NordGen, I modified the "properties.ipt" back to point to the GBIF registry in Copenhagen again. To mimic the registry feature for adding the extension, I made a copy of the file from "http://gbrds.gbif.org/registry/ipt/extensions.json" and added my application schema from the extension as you will see at "http://wwwdev.ngb.se/portal/rs/ipt/extensions.json". The application schema (as defined in "extensions.json") and online from: "http://wwwdev.ngb.se/portal/rs/ipt_germplasm.xml", creates a namespace (for the use by IPT) as well as inclides the URL for the actual draft germplasm extension I made: "http://ipt.gbif.org/extension/germplasm/ http://wwwdev.ngb.se/portal/rs/dwc_germplasm.xsd" The application schema itself (ipt_germplasm.xml) only lists the terms I want to use in IPT, with the property name to be displayed in the IPT mapping interface. To create this file I started with one of the other extensions "http://gbrds.gbif.org/resources/extensions/vernacularName.xml". I just made a copy of this file and replaced the names and terms for vernacular name extension with the terms I wanted from the draft germplasm extension. I hope that my description of what I think it was I did is more or less correct. I copy the IPT mailing list so that Markus and Tim may have a chance to correct me or to add more information to the procedure. Cheers Dag Terje _____ From: Eli Agbayani [mailto:eagbayani@eol.org] To: Dag Terje Filip Endresen [mailto:dag.endresen@nordgen.org] Sent: Tue, 26 May 2009 22:52:35 +0200 Subject: Re: Adding an extension for germplasm to IPT Dear Tag, Thanks for your email. Can you please forward to me the instructions you said you followed in testing your own extension. That is the instructions the GBIF guys gave you. Thanks. Eli ----- Original Message ----- From: "Dag Terje Filip Endresen" <dag.endresen(a)nordgen.org> To: "\"Markus Döring (GBIF)\"" <mdoering(a)gbif.org>, "Eli Agbayani" <eagbayani(a)eol.org> Cc: ipt(a)lists.gbif.org Sent: Friday, May 15, 2009 9:07:29 AM (GMT-0500) America/New_York Subject: Adding an extension for germplasm to IPT Hi Markus and Tim, Thanks a lot for your help! I followed your instructions and successfully added my DRAFT version of a DarwinCore extension for germplasm to the IPT. I have listed a brief summary of each of the steps I followed below. If you are interested, you may visit the IPT from NordGen with a DEMO dataset mapped to terms from this DRAFT Darwin Core extension for germplasm at: http://atlas.nordgen.org/ipt/occResource.html?resource_id=77 1. Schema I built a suggestion to a DRAFT Darwin Core extansion for germplasm http://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germpl… http://wwwdev.ngb.se/portal/rs/dwc_germplasm.xsd 2. XML definition for IPT Listing the terms to use from the suggested DRAFT DarwinCore extension http://wwwdev.ngb.se/portal/rs/ipt_germplasm.xml 3. Add this XML definition to a copy of extensions.json Starting with " http://gbrds.gbif.org/registry/ipt/extensions.json " Add text {"title":"Germplasm","url":" http://wwwdev.ngb.se/portal/rs/ipt_germplasm.xml ","id":9} Saved as: http://wwwdev.ngb.se/portal/rs/ipt/extensions.json 4. Modify ipt.properties PATH_TO_TOMCAT_WEBAPPS/ipt/WEB-INF/classes/ipt.properties Line 7: "registryUrl= http://gbrds.gbif.org/registry " modified to "registryUrl= http://wwwdev.ngb.se/portal/rs " 5. Restart Tomcat (reload ipt) The new ipt.properties settings does not seem to be loaded without restart of tomcat 6. Add/load the new extension to IPT Login with admin permissions http://your_server_name/ipt/admin/extensions.html Click "Check for all available extensions" Select the name of the new extension Select "install" and "Done" 7. Mapping of terms to your data Select the new extension under "Add New Mapping" Click "Add" button to the right Select and map terms I selected the "publish" button and hope that this will not cause this dataset to be registered at the GBIF registry...? Without selecting the "publish" button the dataset is not listed from the menu item "explore". I was missing the option to publish a dataset under this "explore", but not not to register with the GBIF registry...? Should there not be one more step to this procedure? Cheers Dag Terje PS. I have noticed that the right side context menu is very sensitive to missing data (Navigate Taxonomy, Navigate Geography). If some of the higher taxonomic levels is missing I get an error message instead of the context menu. For example I did not have phylum for the genebank dataset and the error message on "Navigate Taxonomy" untill I added data for this term. Similar I did not have continent causing the "Navigate Geography" context menu to start at country. When continent and/or country is missing, the "Navigate Geography" context menu creates a top node for the lowest level available - sometimes even the coordinate is displayed as the top node here. Would be cute if the IPT could default to "unknown continent", "unknown country"; "unknown phylum", ... or something similar. PPS. NB! This DRAFT extension for germplasm is still under development and I am sure that I still duplicate some terms from DarwinCore or other extensions! I did not yet work much with the terms for trait observations on germplasm, but added most of the terms from the new proposed draft standard for these data for the European genebank community. From: "Markus Döring (GBIF)" [mailto: mdoering(a)gbif.org ] To: Dag Terje Filip Endresen [mailto: dag.endresen(a)nordgen.org ], Eli Agbayani [mailto: eagbayani(a)eol.org ] Cc: ipt(a)lists.gbif.org Sent: Wed, 13 May 2009 00:05:33 +0200 Subject: Re: [IPT] IPT connection problem Dag, Eli, I've checked the IPT code again for the extension registry URL and I was actually wrong. The current version *does* make use of the ipt.properties settings. The standard GBIF URL that is used in the ipt.properties should be: registryUrl= http://gbrds.gbif.org/registry The registry then returns a JSON list of all known extensions located at: http://gbrds.gbif.org/registry /ipt/extensions.json So to test your own extensions you can modify this json list to include entries for your own (pointing to your extension xml definitions hosted on some URL), upload that json file to some http server and modify the ipt.properties setting to point to your registry, e.g.: registryUrl= http://dev.eol.org/ipt that will finally point to the file http://dev.eol.org/ipt/ipt/extensions.json To get everything working this registry base URL should also deal with other things, e.g. the registry of resources, organisations, services, etc. But in order to test the extensions this should still work. If you give it a try, please report your findings back to this list. cheers, Markus On May 12, 2009 , at 6:05 PM, Markus Döring (GBIF) wrote: PS. I agree with Jörg that a convenient way to keep the old data directory when upgrading the IPT would be cute. This is indeed the case. We will aim wherever possible to make upgrading as simple as it can be. For bug fix releases, such as this snapshot, with no structural change the data directory can be migrated directly. In future releases, we might require a "one time" migration task be run. I anticipate the first one being required when the DwC standard is ratified. if you look into your ipt.properties file you can modify the following settings: dataDir= ${ipt.datadir} registryUrl= ${ipt.registry.url} the dataDir should be an absolute path pointing to your data dir (defaults to the ipt webapp data subfolder). the registry URL can point to a development registry - unfortunately the extensions and vocabs currently dont use this setting, only the UDDI style registration of resources and organisations. We will make sure that the IPT uses this setting also for the extension registration, so you can easily point it to an alternative extension site for testing. markus --------------------------------------------------------------------- -------- Some more useful instructions from Tim ----------- --------------------------------------------------------------------- _____ From: Tim Robertson [mailto:trobertson@gbif.org] To: Dag Terje Filip Endresen [mailto:dag.endresen@nordgen.org] Cc: ipt(a)lists.gbif.org Sent: Tue, 12 May 2009 15:11:10 +0200 Subject: Re: [IPT] IPT connection problem Hi all, PS. I agree with Jörg that a convenient way to keep the old data directory when upgrading the IPT would be cute. This is indeed the case. We will aim wherever possible to make upgrading as simple as it can be. For bug fix releases, such as this snapshot, with no structural change the data directory can be migrated directly. In future releases, we might require a "one time" migration task be run. I anticipate the first one being required when the DwC standard is ratified. PPS. And a convinient way to add a thematic extension to the DwC (for testing and demonstration) would also be very useful. I am thinking of the draft DwC germplasm extension - as well as a new draft for germplasm trait observation data I have started to work on. I assume this perhaps could be done as an addition in the IPT code somewhere around "WEB-INF/classes/org/gbif/provider/model/" ...? A good suggestion. We should look at setting up some sandbox repository for exactly this purpose. Dag, for testing and demonstration you could do the following, but please be very careful not to register these datasets with GBIF. - The IPT will call (http://gbrds.gbif.org/registry/ipt/extensions.json and http://gbrds.gbif.org/registry/ipt/thesauri.json) to get the extensions and the thesauri. - The response is fairly self explanatory, and for a test, you could override gbrds.gbif.org in you host file, and put up a different version locally for example referencing your test extensions. - Then simply update your extensions through the IPT. - Sorry, not the easiest work around, but might get you able to demonstrate how you can start to build your community without waiting for the sandbox repository. Best wishes, Tim

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Re: [IPT] IPT connection problem
by Tim Robertson 19 May '09

19 May '09

Hi Mickael, Please always post questions to the list, to help us keep an FAQ up to date and allow for others to search etc. I have just tested it myself with the following: Database connection URL: jdbc:mysql://localhost:3306/portal Database User: tim Database Password: password and it worked... so, to get started debugging your issue may I please ask some basic questions: - You wrote "jdbc:mysql://localhost:3306/databasename" - is your database name correct? - You are running the IPT on the same machine as the database? - You are using mysql? Cheers, Tim On 11 May 2009, at 10:26, Mickael Graf wrote: > Hi Tim, > > I'm trying to create a resource in IPT but I encounter a problem while > creating the link to the database: in "Source Data" it is written > under > "SQL Data Sources" I have the message "No Database connected. Please > adjust connection parameters to use SQL sources" while it keeps my > settings correctly. I hope I wrote the jdbc string well: > jdbc:mysql://localhost:3306/databasename. > > I surprised because I am using the same parameters as with TAPIRLink > in > which I don't have any problem. I don't think I should make any > changes > in my grants on my database. > > Cheers, > Mickaël > > -- > --------------------------------- > Mickaël Graf > Database developper, GBIF Sweden - http://www.gbif.se > tel: +46 8 5195 4045 > mailto:mickael.graf@nrm.se > > Swedish Museum of Natural History - http://www.nrm.se > Box 50007 > SE-104 05 Stockholm > Sweden > >

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star schema functionality request
by Eli Agbayani 12 May '09

12 May '09

Markus, Tim, It is a concern for EOL usage of the IPT that the star schema is missing the functionality to add extension to another extension and not just always to the main DWC. The denormalized approach of doing actually this doesn't look good and providers will not like it. Another concern is the size of the recordset if we will (denormalize) repeat the main data object many times to accommodate many references, agents, audience type associated with it. We will continue testing IPT's usage for EOL while trying to minimize the overhead of the denormalized approach. But it would really be helpful to add the functionality making the star schema more relational. Thanks. Eli

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star schema functionality request
by Eli Agbayani 09 May '09

09 May '09

Markus, Tim, It is a concern for EOL usage of the IPT that the star schema is missing the functionality to add extension to another extension and not just always to the main DWC. The denormalized approach of doing actually this doesn't look good and providers will not like it. Another concern is the size of the recordset if we will (denormalize) repeat the main data object many times to accommodate many references, agents, audience type associated with it. We will continue testing IPT's usage for EOL while trying to minimize the overhead of the denormalized approach. But it would really be helpful to add the functionality making the star schema more relational. Thanks. Eli

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IPT test installation
by Michael Denslow 05 May '09

05 May '09

Hello Everyone, I have been attempting to run a demo of the IPT to show some colleagues how the toolkit works. I saw Tim Robertson give a run down of the tool in Virginia a few weeks ago, but I can't seem to recreate this. I am sure that I am missing something obvious here. I go to the Demo site at http://ipt.gbif.org/index.html and create a login and password. Login Then I only have the 'Home' and 'Explore' tabs showing. I am not sure how to start uploading the my example data. Thanks for any help you can provide, Michael -- Michael Denslow Graduate Student I.W. Carpenter Jr. Herbarium [BOON] Department of Biology Appalachian State University Boone, North Carolina U.S.A. -- AND -- Communications Manager Southeast Regional Network of Expertise and Collections sernec.org

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