[Ala-portal] Names Generator Issues

Fri Mar 14 18:19:29 CET 2014

I thank you for the quick answer David and Tim .

We have studied the process to create the namematching index based on the
National List of Australia and I see that reproducing the same process to
create a new National List is quite complex.

But, for now, we just have the demand to include some names that aren´t
included in current namematching index.

If we understood, we need at first, run the Names Generator with the input
of a set of CSVs from APNI, APC e AFD. Based on the output of the Names
Generator we run the Name Mathcing for creating the LUCENE index, right?

If it´s right, it would be great If we could execute this same standard
process, but with de input CSVs modified, with our set of names included in
these CSVs (in the same format).

In the future (after this 3 months) we can study the possibility to
generate our complete National List .

But for now, we need to include a set of names in the namematching index.
It could be possible to be realized in a short time, in one or two weeks?

Best regards,

Allan Koch Veiga

Núcleo de Pesquisa em Biodiversidade e Computação - BioComp
Laboratório de Automação Agrícola - LAA
Depto. de Engenharia de Computação e Sistemas Digitais - PCS
Engenharia Elétrica - Escola Politécnica da USP
Celular: +55 11 8401-2277
Email: allan.kv at usp.br

"*Stay hungry, stay foolish.*" Stewart Brand

2014-03-12 23:15 GMT-03:00 <David.Martin at csiro.au>:

>  Thanks Allan, Paulo, Tim.
>
>  We appreciate your efforts in setting this software upm locally, and
> thanks for emailing the list.
>
>  1) Versioning
>
>  While we are on the track of making this software re-usable by other
> projects/organisations, it is still very early days. Versioning and
> packaging are things that we need to tackle properly in the 3 month
> evaulation period [2] and we are working with GBIF on the best approach
> here (see Tim's email regarding Ansible). To date, the ALA environment
> itself is the only place these components are used in production and we
> manage these closely ourselves. We havent had a need to tightly version
> components, but as other projects become reliant we need to do this
> properly. At this point it time, I'd recommend ignoring developments on
> branches within SVN.
>
>  2) ala-name-generator
>
>  We didn't anticipate that other projects would be using the
> ala-name-generator code at this stage (or at all), and instead would rely
> on the Catalogue of Life names lucene index we've produced [1]. The
> ala-name-generator code as it currently is isnt suitable for use outside
> the Australian context. It is dealing with some of the quirks of Australian
> species lists and merging some elements from different sources. We should
> have marked wikis to that effect.
>
>  That said, we appreciate the need for other projects to use their own
> taxonomic checklists. This was something I'd hope we tackle in the 3 month
> evaluation period [2]. There's a few of potential approaches here we are
> exploring and we'll email this list soon with some progress on this front.
> I suggest in the meantime, projects make use of the existing index [1].
>
>  Thanks again,
>
>  Dave Martin
> ALA
>
>  [1] http://biocache.ala.org.au/archives/col_namematching.tgz
> [2] See GBIF's email sent 21st Feb 2014 - "Biodiversity data portals:
> Using the ALA tooling"
>
>
>   From: "Tim Robertson [GBIF]" <trobertson at gbif.org>
> Date: Thursday, 13 March 2014 2:16 am
> To: Paulo André <pfilipak at gmail.com>
> Cc: "Ala-portal at lists.gbif.org" <Ala-portal at lists.gbif.org>
> Subject: Re: [Ala-portal] Names Generator Issues
>
>   Hi Paulo
>
>  Those are all good comments - I'll make sure the ALA dev team are
> following those issues.
> As this goes forward, it is clear that code releases are going to be
> needed, so we get immutable binaries in nexus and tagged SVN branches.
>  I'll try and raise this with Dave Martin.
>
>  I'll try and follow the resolutions for the issues you log, build an
> artifact and verify the same results.
> I'm not so much into scala, but IIRC I saw that issue with another
> artifact.  The solution was to run this before running the command line:
>   jar -xf ala-names-generator-1.0-SNAPSHOT-assembly.jar lib
>
>  I found this in the way they run the biocache command line tools in:
>
> https://ala-portal.googlecode.com/svn/trunk/biocache-install/ubuntu/install.sh
>
>  It may not be the solution, but worth trying.
>
>  I hope this helps,
> Tim
>
>
>
>  On Mar 12, 2014, at 3:57 PM, Paulo André wrote:
>
>  Tim
>
>  I had have several issues on
> https://code.google.com/p/ala-portal/source/browse/#svn%2Ftrunk%2Fala-names-generator<https://code.google.com/p/ala-portal/source/browse/#svn/trunk/ala-names-generator>
>
>  I wrote on Jira: http://dev.gbif.org/issues/browse/ALA
>
>  []'s
> Paulo Andre Filipak
>
>
> 2014-03-12 11:51 GMT-03:00 Tim Robertson [GBIF] <trobertson at gbif.org>:
>
>>  Hi Allan,
>>
>>  I am sure the ALA folks will comment when they wake up.  But...
>>
>>  It doesn't appear to be published as an artifact in the ALA maven
>> repository:
>>   http://maven.ala.org.au/repository/au/org/ala/
>>
>>  You could build from source from:
>> https://code.google.com/p/ala-portal/source/browse/#svn%2Ftrunk%2Fala-names-generator<https://code.google.com/p/ala-portal/source/browse/#svn/trunk/ala-names-generator>
>>
>>  I presume using something along the lines of "mvn clean
>> assembly:assembly"
>>
>>  I hope this helps provide some options,
>> Tim
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>   On Mar 12, 2014, at 3:32 PM, Allan Koch wrote:
>>
>>    Does anyone knows where I can download this jar:
>> *ala-names-generator-1.0-SNAPSHOT-assembly.jar*?
>>
>> I´m trying to generate a new Taxon Name List based on NSL for the
>> Biocache processing.
>> This instructions has been followed:
>>
>> http://code.google.com/p/ala-portal/wiki/UpgradeALANames
>>
>> According the instructions, I need to run this command:
>>
>> java -Xmx1G -Xms1G -cp .:ala-names-generator-1.0-SNAPSHOT-assembly.jar
>> au.org.ala.names.NamesGenerator --all
>>
>> But, I can´t find this JAR.
>>
>>  We are trying to build the Scala Project, but we are having some
>> troubles.
>> Would help me, for while, if I could run a ready JAR.
>>
>>  Best regards,
>>
>>   Allan Koch Veiga
>>
>> Research Center on Biodiversity and Computing - BioComp
>> University of São Paulo
>>
>> Laboratório de Automação Agrícola - LAA
>> Depto. de Engenharia de Computação e Sistemas Digitais - PCS
>> Engenharia Elétrica - Escola Politécnica da USP
>> Celular: +55 11 98401-2277
>> Email: allan.kv at usp.br
>>
>> "*Stay hungry, stay foolish.*" Stewart Brand
>>     _______________________________________________
>> Ala-portal mailing list
>> Ala-portal at lists.gbif.org
>> http://lists.gbif.org/mailman/listinfo/ala-portal
>>
>>
>>
>> ----------------------------------------------------------------------------------------
>>  Tim Robertson - GBIF Head of Informatics - trobertson at gbif.org
>>  Global Biodiversity Information Facility http://www.gbif.org/
>>  GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
>>  Tel: +45 3532 1487  Mob: +45 2826 1487  Fax: +45 2875 1480
>> ----------------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
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>> Ala-portal at lists.gbif.org
>> http://lists.gbif.org/mailman/listinfo/ala-portal
>>
>>
>
>
> ----------------------------------------------------------------------------------------
>
> Tim Robertson - GBIF Head of Informatics - trobertson at gbif.org
>
> Global Biodiversity Information Facility http://www.gbif.org/
>
> GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
>
> Tel: +45 3532 1487  Mob: +45 2826 1487  Fax: +45 2875 1480
>
>
> ----------------------------------------------------------------------------------------
>
>
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