- ALA-Portal - lists.gbif.org

Getting started with ALA
by Nicolas Noé 14 Mar '15

14 Mar '15

Hi all, I wanted to "take some advance" before Paris Workshop to get familiar with the ALA portal on different aspects: installation, theming, customization, data load, ... I successfully built a VM using the ala-install project and the Ansible/Vagrant scripts, and I am able to access the visitor front page from there. Is there any documentation to tell me how to get from there ? Or should I just wait for the Paris Workshop ? Best, Nicolas

2 1

errors during the ansible script execution
by Marie-Elise Lecoq 13 Mar '15

13 Mar '15

Hi all ! I had some issues with my ALA demo portal on my server so I decided to re-install an installation on VM with vagrant and ansible using the last version of ala-install project (from the ALA github). Unfortunately, I had some errors. The first one was about the vagrant user rights. I added "remote_user: vagrant" and "sudo: yes" on the ala-demo.yml file and it fixed it. Then, I have issues with undefined ansible variables (solr_hostname and biocache_service_hostname) on the vagrant file. I resolved those bugs by adding them in the file. Now, I have another fatal error about another missing variable : userdetails_url. The error message is : fatal: [10.1.1.2] => {'msg': "AnsibleUndefinedVariable: One or more undefined variables: 'userdetails_url' is undefined", 'failed': True} fatal: [10.1.1.2] => {'msg': 'One or more items failed.', 'failed': True, 'changed': False, 'results': [{'msg': "AnsibleUndefinedVariable: One or more undefined variables: 'userdetails_url' is undefined", 'failed': True}]} It seems that this variable is needed on the biocache-config.properties. When I searched this variable on the other files, I found that you filled it with "https://auth.ala.org.au/userdetails/userDetails". I guess that it is linked to the authentication system. In my configuration, what kind of data do I have to fill in this field ? Do you have any clue about what I can do in order to skip this error ? If it is linked to the authentication system, I don't need it on our portal (for now). In this case, how can I remove the system ? I'm not sure that my explanation and my questions are clear :-)! Don't hesitate to ask me more information if you need it. In advance, thanks! Best regards, Marie-Elise --

2 2

Update: David Martin (ALA) on secondment with GBIF
by Tim Robertson 25 Feb '15

25 Feb '15

Dear all, The GBIF Secretariat is very pleased to announce that from mid April David Martin, the lead technical architect of the Atlas of Living Australia (ALA), will be located in the UK and working on secondment with GBIF. One of the objectives of this secondment is to boost support for the international adopters of the ALA tooling, which is underway by several nodes and projects within the GBIF network, and enable technical knowledge exchange from the big data indexing on GBIF.org into the ALA tooling. David will join the ALA developer workshop being at the GBIF European node meeting in Paris on the 5th - 6th May [1], where we aim to discuss and plan for accelerating the deployments and customisations underway for the ALA tools. Anyone wishing to join the workshop should contact the meeting organisers or myself. GBIF are very grateful to CSIRO for offering and funding this placement and look forward to working more closely with David. Many thanks, Tim [1] http://www.gbif.fr/eu_node_meeting_2015/workshop/index

1 0

: Web services: How to obtain the total number of occurrences
by Santiago Martinez de la Riva 06 Nov '14

06 Nov '14

Hi all, Does someone know if there are some call that allows me to obtain the total number of occurrences/records that I have in my portal?? Kind regards, Santi. --------------------------------------------------------------------------------------- Santiago Martínez de la Riva GBIF.ES, Unidad de Coordinación Tel. +34 91 4203017 x 273 Real Jardín Botánico - CSIC Fax +34 91 429 2405 Plaza de Murillo, 2 sama(a)gbif.es 28014 Madrid, Spain www.gbif.es

2 4

[Ala-Portal]: NameIndexer: What's meaning of this WARN...
by Santiago Martinez de la Riva 06 Nov '14

06 Nov '14

Hi all, I'm trying indexing our list of animals, I'm using the nameindexer tool and I see this WARN: 2014-11-05 12:08:10,639 WARN : [ALANameIndexer] - urn:lsid:catalogueoflife.org:taxon:fcb73025-ac8e-11e3-805d-020044200006:col20140822 Humeralis has issues creating a soundex: String index out of range: -1 This is the record: id parentNameUsageID acceptedNameUsageID scientificName kingdom phylum class order family genus specificEpithet infraspecificEpithet taxonRank scientificNameAuthorship nomenclaturalCode taxonomicStatus nomenclaturalStatus occurrenceStatus taxonID 7810593 urn:lsid:catalogueoflife.org:taxon:e49d1280-ac8e-11e3-805d-020044200006:col20140822 urn:lsid:catalogueoflife.org:taxon:fcb73025-ac8e-11e3-805d-020044200006:col20140822 X humeralis Hust. , 1924 Animalia Arthropoda Insecta Coleoptera Curculionidae X humeralis species Hust. , 1924 provisionally accepted name urn:lsid:catalogueoflife.org:taxon:fcb73025-ac8e-11e3-805d-020044200006:col20140822 What is the problem? Kind regards, Santi. --------------------------------------------------------------------------------------- Santiago Martínez de la Riva GBIF.ES, Unidad de Coordinación Tel. +34 91 4203017 x 273 Real Jardín Botánico - CSIC Fax +34 91 429 2405 Plaza de Murillo, 2 sama(a)gbif.es 28014 Madrid, Spain www.gbif.es

1 0

Re: [Ala-portal] A little doubt about SOLR/JVM configuration
by David.Martin＠csiro.au 10 Oct '14

10 Oct '14

Thanks Santi. I've cc-ed the list as this is probably a common question. The memory allocation can be manipulated in the scripts [1]. On Debian (Ubuntu) machines this manipulates the config in this file: /etc/default/tomcat7 and specifically the line: JAVA_OPTS="-Xmx2g -Xms2g -XX:MaxPermSize=256m -Xss256k" For production systems, if you have the ability to use more than 1 machine, I would recommend setting up SOLR on a separate machine. Theres a playbook for this here [2]. The biocache can point to a different SOLR server by changing the following property in /data/biocache/config/biocache-config.properties # The URL of SOLR services. In the case of embedded SOLR (no for production), this could be a directory path instead solr.home=http://localhost:8080/solr Cheers Dave Martin [1] https://github.com/AtlasOfLivingAustralia/ala-install/blob/master/ansible/r… [2] https://github.com/AtlasOfLivingAustralia/ala-install/blob/master/ansible/s… ________________________________________ From: Santiago Martinez de la Riva [sama(a)gbif.es] Sent: 09 October 2014 20:14 To: Martin, Dave (NRCA, Black Mountain) Subject: RE: [Ala-portal] A little doubt about SOLR/JVM configuration Hi Dave, Im sure that with you experience you can help me with this topic. Now I'm having this problem with solr and jvm: ERROR SolrCore org.apache.solr.common.SolrException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space I think that I have to config JVM_ARG to assign more memory to the Java heap, but if I'm executing JAVA in a VM with 32 GB and SOLR is consuming more or less 14GB with 10 millions of records. What do you recommend me to assign to Java Heap. Export JVM_ARGS="-Xmx YYYY m -XX:MaxPermSize= ZZZZ m" Thanks in advance, Santi.

1 0

biocache-hubs customizations
by Santiago Martinez de la Riva 04 Oct '14

04 Oct '14

Hi all, I have two questions: First: I want to change some FacetNames such as State/Territory, Local Govt. Area in the _advanced.gsp, but I don't know where is located this information. Could you give some tip? and second: If I modify the biocache-hub plug-in how can i do that generic-hub uses my new biocache-hub? Thanks so muchh!!! Kind regards, Santi. --------------------------------------------------------------------------------------- Santiago Martínez de la Riva GBIF.ES, Unidad de Coordinación Tel. +34 91 4203017 x 273 Real Jardín Botánico - CSIC Fax +34 91 429 2405 Plaza de Murillo, 2 sama(a)gbif.es 28014 Madrid, Spain www.gbif.es

3 11

ProviderCode Maps: Indexing dataset with several collection code
by Santiago Martinez de la Riva 02 Oct '14

02 Oct '14

Dear all, I have some datasets which have several collection code, the question is: how can i do to create the right relationship between the dataset, the collection and the instituttion through the ProviderCodes Map, if the dataset has 2 or more collection code?? e.g: If the dataset has these collection codes: cof and co_cof. I create the provider code: cof co_cof or cof, co_cof after this I create the providerCode Map between the institution and the colecction, and I select the codes, and I don't select the checkbox "Exact". But when I process and index again the dataset, I don't get that this process indexes all the records that dataset has. Could you help please? Cheers, Santi. --------------------------------------------------------------------------------------- Santiago Martínez de la Riva GBIF.ES, Unidad de Coordinación Tel. +34 91 4203017 x 273 Real Jardín Botánico - CSIC Fax +34 91 429 2405 Plaza de Murillo, 2 sama(a)gbif.es 28014 Madrid, Spain www.gbif.es

2 2

Crowdin project: translations of collectory module.
by Santiago Martinez de la Riva 01 Oct '14

01 Oct '14

Hi all, I forgot to tell that we finished to translate the message.properties file of collectory module in the crowdin platform two weeks ago. https://crowdin.com/project/ala-i18n/es-ES I have to say that not all of this translations are exactly right becouse when you load the message properties file in the collectory module you need to move the position of some message variables. This is because sometimes the position of the variables are not the same in both language, in this case in spanish and english, and I think that this issue will occur in other languages. Kind regards, Santi --------------------------------------------------------------------------------------- Santiago Martínez de la Riva GBIF.ES, Unidad de Coordinación Tel. +34 91 4203017 x 273 Real Jardín Botánico - CSIC Fax +34 91 429 2405 Plaza de Murillo, 2 sama(a)gbif.es 28014 Madrid, Spain www.gbif.es

1 0

Taxon Profile DB
by Allan Koch 30 Sep '14

30 Sep '14

Hi all, I was studing the code of Processing of biocache-store and I figured out that the biocache uses the TaxonProfile list to include Vernacular names from a scientific name ID. Is it right? If yes, how can I create or modify the TaxonProfile? I also figured out that TaxonProfile list is storaged in Cassandra ("Taxon" family collumn). Is this database filled by *TaxonProfileLoader* ( https://github.com/AtlasOfLivingAustralia/biocache-store/blob/master/src/ma… How to run this TaxonProfileLoader and with what input? or I might consider creating a Cassandra script for inserting records into the Taxon family columns? Thank you folks, 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(a)usp.br

1 0