April 2014 - ALA-Portal - lists.gbif.org

DwC-A loading problems
by Daniel Lins 26 Jun '14

26 Jun '14

Hi Nick and Dave, We are having some problems in Biocache during the upload of DwC-A files. As shown below, after run the method "au.org.ala.util.DwCALoader", our system returns the error message "Exception in thread "main" org.gbif.dwc.text.UnkownDelimitersException: Unable to detect field delimiter" I accomplished tests using DwC-A files with tab-delimited text files and comma-delimited text files. In both cases the error generated was the same. What causes these problems? (** CSV Loader works great) *tab-delimited file test* poliusp@poliusp-VirtualBox:~/dev/biocache$ s*udo java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7 -l /data/collectory/upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b.zip* 2014-04-28 01:44:02,837 INFO : [ConfigModule] - Loading configuration from /data/biocache/config/biocache-config.properties 2014-04-28 01:44:03,090 INFO : [ConfigModule] - Initialise SOLR 2014-04-28 01:44:03,103 INFO : [ConfigModule] - Initialise name matching indexes 2014-04-28 01:44:03,605 INFO : [ConfigModule] - Initialise persistence manager 2014-04-28 01:44:03,606 INFO : [ConfigModule] - Configure complete Loading archive /data/collectory /upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b.zip for resource dr7 with unique terms List(dwc:occurrenceID) stripping spaces false incremental false testing false *Exception in thread "main" org.gbif.dwc.text.UnkownDelimitersException: Unable to detect field delimiter* at org.gbif.file.CSVReaderFactory.buildArchiveFile( CSVReaderFactory.java:129) at org.gbif.file.CSVReaderFactory.build(CSVReaderFactory.java:46) at org.gbif.dwc.text.ArchiveFactory.readFileHeaders( ArchiveFactory.java:344) at org.gbif.dwc.text.ArchiveFactory.openArchive(ArchiveFactory.java: 289) at au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129) at au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106) at au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52) at au.org.ala.util.DwCALoader.main(DwCALoader.scala) *comma-delimited file test* poliusp@poliusp-VirtualBox:~/dev/biocache$ *sudo java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7 -l ./dwca-teste3.zip* 2014-04-28 01:56:04,683 INFO : [ConfigModule] - Loading configuration from /data/biocache/config/biocache-config.properties 2014-04-28 01:56:04,940 INFO : [ConfigModule] - Initialise SOLR 2014-04-28 01:56:04,951 INFO : [ConfigModule] - Initialise name matching indexes 2014-04-28 01:56:05,437 INFO : [ConfigModule] - Initialise persistence manager 2014-04-28 01:56:05,438 INFO : [ConfigModule] - Configure complete Loading archive ./dwca-teste3.zip for resource dr7 with unique terms List( dwc:occurrenceID) stripping spaces false incremental false testing false *Exception in thread "main" org.gbif.dwc.text.UnkownDelimitersException: Unable to detect field delimiter* at org.gbif.file.CSVReaderFactory.buildArchiveFile( CSVReaderFactory.java:129) at org.gbif.file.CSVReaderFactory.build(CSVReaderFactory.java:46) at org.gbif.dwc.text.ArchiveFactory.readFileHeaders( ArchiveFactory.java:344) at org.gbif.dwc.text.ArchiveFactory.openArchive(ArchiveFactory.java: 289) at au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129) at au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106) at au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52) at au.org.ala.util.DwCALoader.main(DwCALoader.scala) Thanks! Regards. -- Daniel Lins da Silva (Mobile) 55 11 96144-4050 Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br daniel.lins(a)gmail.com

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Re: [Ala-portal] Cas Authentication - Hubs-Webapp
by Suelane G. Fontes 28 Apr '14

28 Apr '14

6 13

Cas Authentication - Hubs-Webapp
by Suelane G. Fontes 16 Apr '14

16 Apr '14

2 1

ala-cas
by Paulo André 15 Apr '14

15 Apr '14

Hi guys We'd like to deploy ala-cas and we've read documentation: https://code.google.com/p/ala-bie/wiki/Authentication It says to use ala-cas 2.0 version, but we've seen on source code the file pom.xml do reference for 1.0-SNAPSHOT version. How can we get ala-cas 2.0 version? BR Paulo Andre Filipak

2 1

tomcat authentication
by Paulo André 13 Apr '14

13 Apr '14

Hi guys We've used ala-hubs and it works perfectly. Now we would like to authenticate through tomcat (basic authentication). It works well, too. We are going to first page on ala-hubs. But, when we've clicked on search button there is not response. Have you ever used tomcat authentication? BR Paulo André Filipak

2 2

NSL
by Allan Koch 11 Apr '14

11 Apr '14

Hi Natasha and David, I would like to notify that the DwC-A names indexer works perfectly. We already have the Biocache running with a customized taxon concepts list. We are planning automate the process to create and update the index by merging several lists (CoL, Fauna, Flora, etc). When it is ready, we will let you know. Thanks for supporting. ------------------------------------------------------------------------ But now, we are working in the list of taxon of BIE. If I understood right, the BIE consumes a NSL-WS as the source of taxon concepts, right? So, If we want an instance of BIE with our customized taxon concepts list, will we need to run an instance of the NSL project and create a new names repository in an XML DB (eXist)? I have attached a figure that describes what we have understanding the architecture. Could you validate if it´s correct? 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(a)usp.br "*Stay hungry, stay foolish.*" Stewart Brand

1 0

cassandra
by Paulo André 11 Apr '14

11 Apr '14

Hi We've been used Cassandra 1.2.8 on Ala-portal. https://code.google.com/p/ala-portal/wiki/GettingStarted?tm=6 Now, we are going deploy Ala-bie, but it use Cassandra 1.0.7. https://code.google.com/p/ala-bie/wiki/BieInitialSetup Could we use Cassandra 1.2.8 on both applications? Is it possible? BR Paulo André Filipak

3 2

internationalization problems
by Suelane G. Fontes 09 Apr '14

09 Apr '14

3 9

Names Generator Issues
by Allan Koch 03 Apr '14

03 Apr '14

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(a)usp.br "*Stay hungry, stay foolish.*" Stewart Brand

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