Re: [Ala-portal] DwC-A loading problems

9 May 2014


      Thanks Daniel.
I've spotted the problem:
java -cp .:biocache.jar au.org.ala.util.DwcCSVLoader dr0 -l dataset-updated.csv -b true
this bypasses lookups against the collectory for the metadata.
To load this dataset, you can use the biocache commandline tool like so:
$ java -cp /usr/lib/biocache:/usr/lib/biocache/biocache-store-1.1-assembly.jar -Xms2g -Xmx2g au.org.ala.biocache.cmd.CommandLineTool
----------------------------
| Biocache management tool |
----------------------------
Please supply a command or hit ENTER to view command list.
biocache> ingest dr8
This will:
1) Retrieve the metadata from the configured instance of the collectory
2) Load, process, sample (if there are layers configured and available) and index
Cheers
Dave
________________________________
From: Daniel Lins [daniel.lins@gmail.com]
Sent: 09 May 2014 14:27
To: Martin, Dave (CES, Black Mountain)
Cc: ala-portal@lists.gbif.org; dos Remedios, Nick (CES, Black Mountain); Pedro Corrêa; Nicholls, Miles (CES, Black Mountain)
Subject: Re: [Ala-portal] DwC-A loading problems
David,
The dr0 configuration:
https://www.dropbox.com/s/lsy11jadwmyghjj/collectoryConfig1.png
Sorry, but this server doesn't have external access yet.
2014-05-09 1:06 GMT-03:00 <David.Martin@csiro.aumailto:David.Martin@csiro.au>:
As an example of what it should look like, see:
http://ala-demo.gbif.org/collectory/dataResource/edit/dr8?page=contribution
________________________________
From: Daniel Lins [daniel.lins@gmail.commailto:daniel.lins@gmail.com]
Sent: 09 May 2014 13:59
To: Martin, Dave (CES, Black Mountain)
Cc: ala-portal@lists.gbif.orgmailto:ala-portal@lists.gbif.org; dos Remedios, Nick (CES, Black Mountain); Pedro Corrêa; Nicholls, Miles (CES, Black Mountain)
Subject: Re: [Ala-portal] DwC-A loading problems
Thanks David,
We use the DwC term "occurrenceID" to identify the records. It's a unique key.
However, when I reload a dataset to update some DwC terms of the records, the system duplicates this data (keeps the old record and creates another with changes).
For instance (update of locality).
Load 1 ($ java -cp .:biocache.jar au.org.ala.util.DwcCSVLoader dr0 -l dataset.csv -b true)
{OccurrenceID: 1, municipality: Sao Paulo, ...},
{OccurrenceID: 2, municipality: Sao Paulo, ...}
Process 1 (biocache$ process dr0)
Index 1 (biocache$ index dr0)
Load 2 (updated records and new records) (($ java -cp .:biocache.jar au.org.ala.util.DwcCSVLoader dr0 -l dataset-updated.csv -b true)
{OccurrenceID: 1, municipality: Rio de Janeiro, ...},
{OccurrenceID: 2, municipality: Rio de Janeiro, ...},
{OccurrenceID: 3, municipality: Sao Paulo, ...}
Process 2 (biocache$ process dr0)
Index 2 (biocache$ index dr0)
Results shown by ALA:
{OccurrenceID: 1, municipality: Sao Paulo, ...},
{OccurrenceID: 2, municipality: Sao Paulo, ...},
{OccurrenceID: 1, municipality: Rio de Janeiro, ...},
{OccurrenceID: 2, municipality: Rio de Janeiro, ...}
{OccurrenceID: 3, municipality: Sao Paulo, ...}
But I expected:
{OccurrenceID: 1, municipality: Rio de Janeiro, ...},
{OccurrenceID: 2, municipality: Rio de Janeiro, ...}
{OccurrenceID: 3, municipality: Sao Paulo, ...}
I need to delete (delete-resource function) existing data before the reload? If no, what I did wrong to generate this data duplication?
Thanks!
Regards,
Daniel Lins da Silva
(Mobile) 55 11 96144-4050tel:55%2011%2096144-4050
Research Center on Biodiversity and Computing (Biocomp)
University of Sao Paulo, Brazil
daniellins@usp.brmailto:daniellins@usp.br
daniel.lins@gmail.commailto:daniel.lins@gmail.com
2014-05-07 0:46 GMT-03:00 <David.Martin@csiro.aumailto:David.Martin@csiro.au>:
Thanks Daniel. Natasha has now left the ALA.
The uniqueness of records is determined by information stored in the collectory. See screenshot [1].
By default, "catalogNumber" is used but you can change this to any number of fields that should be stable in the data.
Using unstable fields for the ID isn't recommended (e.g. scientificName).  To update the records, the process is to just re-load the dataset.
Automatically loaded - this isnt in use and we may remove from the UI in future iterations.
Incremental Load - affects the sample/process/index steps to only run these against the new records.  Load is always incremental based on the key field(s) but if the incremental load box isn’t checked it runs the sample/process/index steps against the whole data set. This can cause a large processing overhead when there’s a minor update to a large data set.
Cheers
Dave Martin
ALA
[1] http://bit.ly/1g72HFN
________________________________
From: Daniel Lins [daniel.lins@gmail.commailto:daniel.lins@gmail.com]
Sent: 05 May 2014 15:39
To: Quimby, Natasha (CES, Black Mountain)
Cc: ala-portal@lists.gbif.orgmailto:ala-portal@lists.gbif.org; dos Remedios, Nick (CES, Black Mountain); Martin, Dave (CES, Black Mountain); Pedro Corrêa
Subject: Re: [Ala-portal] DwC-A loading problems
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 96144-4050tel:55%2011%2096144-4050
Research Center on Biodiversity and Computing (Biocomp)
University of Sao Paulo, Brazil
daniellins@usp.brmailto:daniellins@usp.br
daniel.lins@gmail.commailto:daniel.lins@gmail.com
2014-04-28 3:52 GMT-03:00 Daniel Lins <daniel.lins@gmail.commailto: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 96144-4050tel:55%2011%2096144-4050
Research Center on Biodiversity and Computing (Biocomp)
University of Sao Paulo, Brazil
daniellins@usp.brmailto:daniellins@usp.br
daniel.lins@gmail.commailto:daniel.lins@gmail.com
2014-04-28 3:26 GMT-03:00 <Natasha.Quimby@csiro.aumailto: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:
sudo 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 biocache automatically 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:
sudo 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.commailto:daniel.lins@gmail.com>
Date: Monday, 28 April 2014 3:54 PM
To: "ala-portal@lists.gbif.orgmailto:ala-portal@lists.gbif.org" <ala-portal@lists.gbif.orgmailto:ala-portal@lists.gbif.orgmailto:ala-portal@lists.gbif.orgmailto:ala-portal@lists.gbif.orgmailto:ala-portal@lists.gbif.orgmailto:ala-portal@lists.gbif.org>, "dos Remedios, Nick (CES, Black Mountain)" <Nick.Dosremedios@csiro.aumailto:Nick.Dosremedios@csiro.au>, "Martin, Dave (CES, Black Mountain)" <David.Martin@csiro.aumailto: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$ sudo 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 96144-4050tel:55%2011%2096144-4050
Research Center on Biodiversity and Computing (Biocomp)
University of Sao Paulo, Brazil
daniellins@usp.brmailto:daniellins@usp.br
daniel.lins@gmail.commailto:daniel.lins@gmail.com
--
Daniel Lins da Silva
(Cel) 11 6144-4050
daniel.lins@gmail.commailto:daniel.lins@gmail.com
--
Daniel Lins da Silva
(Cel) 11 6144-4050
daniel.lins@gmail.commailto:daniel.lins@gmail.com
--
Daniel Lins da Silva
(Cel) 11 6144-4050
daniel.lins@gmail.commailto:daniel.lins@gmail.com
--
Daniel Lins da Silva
(Cel) 11 6144-4050
daniel.lins@gmail.commailto:daniel.lins@gmail.com

Re: [Ala-portal] DwC-A loading problems

David.Martin＠csiro.au