Hi Natasha,
It would be great. We have 109 species that we need to include in the current name matching index.
It would be great if you send me a DwC-A with CoL names. I will need just to add these 109 species in that archive in the same format, right?
How will work this proposed solution? Will you provide a souce code, a compiled program (JAR) or we will send to you the DwC-A and you will generate the Lucene index?
Thank you very much for helping.
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@usp.br
"*Stay hungry, stay foolish.*" Stewart Brand
2014-03-17 3:12 GMT-03:00 Natasha.Quimby@csiro.au:
Hi Allan,
The ala-name-generator is useful if you want to use the Australian National Species list as the main source for your namematching index. We would not suggest using this to supplement the name matching index with additional species.
In order to support custom species lists we are planning an enhancement to generate the namematching index from a DarwinCore Archive. We would envision that all the species would be provided as a single DWCA with the attached meta.xml. We think that this could be achieved in the 1-2 week window that you mentioned. We could provide a DWCA which contains Catalogue of Life as a basis for you to start with. You can then add additional names to the DWCA as you please. Do you think that this would suit you needs?
Regards Natasha
From: Allan Koch allan.kv@gmail.com Date: Saturday, 15 March 2014 4:19 AM To: "Martin, Dave (CES, Black Mountain)" David.Martin@csiro.au
Cc: "Ala-portal@lists.gbif.org" Ala-portal@lists.gbif.org Subject: Re: [Ala-portal] Names Generator Issues
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@usp.br
"*Stay hungry, stay foolish.*" Stewart Brand
2014-03-12 23:15 GMT-03:00 David.Martin@csiro.au:
Thanks Allan, Paulo, Tim.
We appreciate your efforts in setting this software upm locally, and thanks for emailing the list.
- 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.
- 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@gbif.org Date: Thursday, 13 March 2014 2:16 am To: Paulo André pfilipak@gmail.com Cc: "Ala-portal@lists.gbif.org" Ala-portal@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....
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-...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@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-...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@usp.br
"*Stay hungry, stay foolish.*" Stewart Brand _______________________________________________ Ala-portal mailing list Ala-portal@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ala-portal
Tim Robertson - GBIF Head of Informatics - trobertson@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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Tim Robertson - GBIF Head of Informatics - trobertson@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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