[Ala-portal] Installation page updated

Santiago sama at gbif.es
Thu May 29 12:04:46 CEST 2014

Dear David,


Thanks so much for the info. I´ll check it on my VM.


Kind regards.



De: David.Martin at csiro.au [mailto:David.Martin at csiro.au] 
Enviado el: jueves, 29 de mayo de 2014 11:43
Para: Santiago Martinez de la Riva; bko at gbif.org
CC: Ala-portal at lists.gbif.org
Asunto: RE: [Ala-portal] Installation page updated


Thanks Santiago, Burke. 


The recommended approach for all projects is to load data following the
instructions that Burke included in his last email [1].

One of the requirements for this to work is that an instance of the
collectory is installed.

What Natasha described (and which is now out of date) is a mechanism for
loading data without a collectory instance. This is useful for local
development purposes only.

This can be done on the command line with version 1.1 with the command:


biocache>> load-local-csv dr0 /tmp/my-csv.txt


The way we load data in our production environment is as follows:


1) Create a data resource in the collectory

2) Upload a CSV or DwC-A zip file into the collectory using the "Upload
file" option

3) Use the command line tool describe in [1] to load, sample (optional),
process and index the data


Hope this helps.


Dave Martin


[1]  <https://code.google.com/p/ala-portal/wiki/LoadBiocacheData>



From: ala-portal-bounces at lists.gbif.org [ala-portal-bounces at lists.gbif.org]
on behalf of Santiago [sama at gbif.es]
Sent: 29 May 2014 19:08
To: 'Burke Chih-Jen Ko [GBIF]'
Cc: Ala-portal at lists.gbif.org
Subject: Re: [Ala-portal] Installation page updated

Hi Burke,


I think that you can use  the instructions that you refer in your mail when
you are running from inside CSIRO/ALA, please someone correct me if I’m


I´m going to tell you my experience:


When I want to index a resource I use biocache.jar. I use two options: Load
a resource via CSV or via Dwc-A. I attach a mail in which Natasha explains
how we can load a resource via Dwc-A.


If I want to load a resource through CSV, I execute the next command:


java -cp .:biocache.jar au.org.ala.util.DwcCSVLoader drtest -l
path-to-file.csv -b true


When you have loaded the resource you have to enter in the biocache command
line, then you must execute “ >biocache” and then you can process and index
the loaded resource. “> process drtest” and “>index drtest”.


My problem  is that when I want to load a resource via Dwc-A and I execute:
java -cp .:biocache.jar au.org.ala.util.DwCALoader drtest

The system doesn’t find the class:  au.org.ala.util.DwCALoader. It´s very


Could you check if you can do this? I mean, could you check if you can load
a resource in the way Natasha explained in her mail?


The mappings. I don’t understand one thing. How is it possible that in the
69f8ef36273, I can see the information in the right way? This is an example
of a Spanish resource from GBIF.org. The occurrences are been loaded,
processed and indexed. How is that in our installation we must to do
something else if in that installation we can see the indexed occurrences
correctly, It is the same installation, right??


Kind regards.




De: Burke Chih-Jen Ko [GBIF] [mailto:bko at gbif.org] 
Enviado el: jueves, 29 de mayo de 2014 9:48
Para: Santiago Martinez de la Riva
CC: Ala-portal at lists.gbif.org
Asunto: Re: [Ala-portal] Installation page updated


Hi Sama,


Yes I did but I use country DwC-A downloaded from GBIF Portal. I basically
follow the instruction on
https://code.google.com/p/ala-portal/wiki/LoadBiocacheData. Precisely it's
done inside the ubuntu box.


After that I can see indexed records but for now it seems the mapping needs
some configuration. I am still looking for configurations.


Did you get the map shown before?






On May 28, 2014, at 5:43 PM, sama <sama at gbif.es> wrote:


Hash: SHA1

Dear Burke,

Have you tried indexing a resource through their DwCA using
biocache-store tool on Mac OS?

Kind Regard.
- ------------------------------------------------------------
Santiago Martínez de la Riva Vivanco
GBIF.ES, Unidad de Coordinación
Real Jardín Botánico CSIC
Plaza de Murillo, 2
28014 Madrid, Spain
Tel: +34 91 4293917 x 273 - sama at gbif.es - www.gbif.es -

El 28/05/2014 17:34, Burke Chih-Jen Ko [GBIF] escribió:

Dear list members,
(Sorry for cross-posting.)

I would like to let you know that we've just updated these two pages on the

1. Essential tools and environment configurations:
2. Installation:

We are able to install the ALA portal demo by following these steps. Any
suggestions on improving the documentation are highly appreciated!



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