[IPT] Adding an extension for germplasm to IPT

Fri May 15 15:12:45 CEST 2009

This is really excellent to see Dag - really well done and thank you  
for taking the time to post those instructions.

Tim

On 15 May 2009, at 15:07, Dag Terje Filip Endresen wrote:

> 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/germplasm/dwc_germplasm.xsd
>     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 at gbif.org]
> To: Dag Terje Filip Endresen [mailto:dag.endresen at nordgen.org], Eli  
> Agbayani [mailto:eagbayani at eol.org]
> Cc: ipt at 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
>>
>>
>
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