[IPT] Adding an extension for germplasm to IPT

Fri May 15 15:07:29 CEST 2009

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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