Hi Natasha,
I managed to import the DwC-A file following the steps reported in the previous email. Thank you!
However, when I tried to update some metadata of an occurrence record (already stored in the database), the system created a new record with these duplicated information. So I started to have several records with the same occurrenceID (I did set in the data resource configuration to use "OcurrenceID" to uniquely identify a record).
How can I update existing records in the database? For instance, the location's metadata of an occurrence record stored in my database?
I also would like to better understand the behavior of the properties "Automatically loaded" and "Incremental Load".
Thanks!!
Regards,
Daniel Lins da Silva (Mobile) 55 11 96144-4050 Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins@usp.br daniel.lins@gmail.com
2014-04-28 3:52 GMT-03:00 Daniel Lins daniel.lins@gmail.com:
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@usp.br daniel.lins@gmail.com
2014-04-28 3:26 GMT-03:00 Natasha.Quimby@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@gmail.com Date: Monday, 28 April 2014 3:54 PM To: "ala-portal@lists.gbif.org" <ala-portal@lists.gbif.orgala-portal@lists.gbif.orgala-portal@lists.gbif.orgala-portal@lists.gbif.orgala-portal@lists.gbif.org
, "dos Remedios, Nick (CES, Black Mountain)" <Nick.Dosremedios@csiro.au , "Martin, Dave (CES, Black Mountain)" David.Martin@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@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@usp.br daniel.lins@gmail.com
-- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins@gmail.com