[Ala-portal] DwC-A loading problems

[Daniel Lins]

Thanks Natasha!

I will try your recommendations. Once finished, I will contact you.

Regards

Daniel Lins da Silva
(Mobile) 55 11 96144-4050
Research Center on Biodiversity and Computing (Biocomp)
University of Sao Paulo, Brazil
daniellins at usp.br
daniel.lins at gmail.com



2014-04-28 3:26 GMT-03:00 <Natasha.Quimby at csiro.au>:

>  Hi Daniel,
>
>  When you specify a local DwcA Load the archive needs to be unzipped. Try
> unzipping *2f676abc-4503-489e-8f0c-fcb6e1bc554b.zip *and then running the
> following:
> s*udo** java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7 -l
> /data/collectory/upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b*
>
>  If you configure the collectory to provide the dwca the biocacheautomatically unzips the archive for you.  You would need to configure dr7
> with the following connection parameters:
>
>  "protocol":"DwCA"
> "termsForUniqueKey":["occurrenceID"],
> "url":"file:////data/collectory/upload/
> 1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b.zip"
>
>  You could then load the resource by:
> s*udo** java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7*
>
>  If you continue to have issues please let us know.
>
>  Hope that this helps.
>
>  Regards
> Natasha
>
>   From: Daniel Lins <daniel.lins at gmail.com>
> Date: Monday, 28 April 2014 3:54 PM
> To: "ala-portal at lists.gbif.org" <ala-portal at lists.gbif.org<ala-portal at lists.gbif.org>
> >, "dos Remedios, Nick (CES, Black Mountain)" <Nick.Dosremedios at csiro.au>,"Martin, Dave (CES, Black Mountain)" <
> David.Martin at csiro.au>
> Subject: [Ala-portal] DwC-A loading problems
>
>   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 at 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$.main(DwCALoader.scala:52)
>         at au.org.ala.util.DwCALoader.main(DwCALoader.scala)
>
>
>  *comma-delimited file test*
>
>  poliusp at poliusp-VirtualBox:~/dev/biocache$ *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 at usp.br
> daniel.lins at gmail.com
>
>


-- 
Daniel Lins da Silva
(Cel) 11 6144-4050
daniel.lins at gmail.com
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