Hi Daniel,
From what you've said, Im not clear on what customisations you have made so its difficult to make a call on the impact of migrating to 1.1. We also do not know what subversion revisions you started with.
We can tell you that functionally there wasn't a great deal of difference between the later snapshots of 1.0 and 1.1. The changes where largely structural i.e. a clean up of packages, removal of redundant code. We did this largely because we needed to (this code base is now over 5 years old) and we wanted to clean things up before other projects started to work with the software.
Upgrading to biocache-service 1.1 and biocache-store shouldnt require any changes to cassandra, but it may require and upgrade of SOLR. If this is the case, you'll need to regenerate your index using the biocache commandline tool. Upgrading to 1.1 shouldnt require any changes to hubs-webapp if you've customised this component.
I'd really recommend move to 1.1 sooner rather than later as it'll give you a stable baseline to work against.
Hope this helps,
Dave Martin ALA
________________________________ From: Daniel Lins [daniel.lins@gmail.com] Sent: 18 June 2014 15:54 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
Hi Dave,
How can I update the Biocache-1.0-SNAPSHOT to the version 1.1? I updated the biocache-store (biocache.jar) and the config file (/data/biocache/conf/config.properties-biocache) but I still have problems. Which other steps I need to do? Apparently this new version of the biocache configuration file generates impacts directly in my Biocache-Services and Solr.
This update will generate some impacts in other components?
I cannot use the installation process based on the Vagrant/Ansible because our environment is different and already have customizations. So I would like to update the biocache with minimum impact, if possible. After we will have to plan the update of the other components.
Can you advise me as to the best way forward?
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
2014-05-26 3:58 GMT-03:00 <David.Martin@csiro.aumailto:David.Martin@csiro.au>: Thanks Daniel.
I'd recommend upgrading to 1.1 and I'd recommend installation with the ansible scripts. This will give you base line configuration. The scripts can be tested on a local machine using vagrant. The configuration between 1.0 and 1.1 changed significantly - removal of redundant, legacy properties, adoption of standard format for property names. Heres the template used for the configuration file in the ansible scripts:
https://github.com/gbif/ala-install/blob/master/ansible/roles/biocache-servi...
Cheers
Dave Martin ALA
________________________________ From: Daniel Lins [daniel.lins@gmail.commailto:daniel.lins@gmail.com] Sent: 26 May 2014 15:02 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
Hi Dave,
When I ran the ingest command (ingest dr0), the system showed errors like these below. However, after the error messages, I ran the index command (index dr0), and data were published on the Portal.
2014-05-20 14:15:05,412 ERROR: [Grid] - cannot find GRID: /data/ala/data/layers/ready/diva/worldclim_bio_19 2014-05-20 14:15:05,414 ERROR: [Grid] - java.io.FileNotFoundException: /data/ala/data/layers/ready/diva/worldclim_bio_19.gri (No such file or directory) at java.io.RandomAccessFile.open(Native Method) at java.io.RandomAccessFile.<init>(RandomAccessFile.java:241) at java.io.RandomAccessFile.<init>(RandomAccessFile.java:122) at org.ala.layers.intersect.Grid.getValues3(Grid.java:1017) at org.ala.layers.intersect.SamplingThread.intersectGrid(SamplingThread.java:112) at org.ala.layers.intersect.SamplingThread.sample(SamplingThread.java:97) at org.ala.layers.intersect.SamplingThread.run(SamplingThread.java:67)
2014-05-20 14:15:05,447 INFO : [Sampling] - ********* END - TEST BATCH SAMPLING FROM FILE *************** 2014-05-20 14:15:05,496 INFO : [Sampling] - Finished loading: /tmp/sampling-dr0.txt in 49ms 2014-05-20 14:15:05,496 INFO : [Sampling] - Removing temporary file: /tmp/sampling-dr0.txt 2014-05-20 14:15:05,553 INFO : [Consumer] - Initialising thread: 0 2014-05-20 14:15:05,575 INFO : [Consumer] - Initialising thread: 1 2014-05-20 14:15:05,575 INFO : [Consumer] - Initialising thread: 2 2014-05-20 14:15:05,577 INFO : [Consumer] - In thread: 0 2014-05-20 14:15:05,579 INFO : [Consumer] - Initialising thread: 3 2014-05-20 14:15:05,579 INFO : [ProcessWithActors] - Starting with dr0| endingwith dr0|~ 2014-05-20 14:15:05,581 INFO : [Consumer] - In thread: 2 2014-05-20 14:15:05,581 INFO : [Consumer] - In thread: 1 2014-05-20 14:15:05,584 INFO : [Consumer] - In thread: 3 2014-05-20 14:15:05,592 INFO : [ProcessWithActors] - Initialised actors... 2014-05-20 14:15:05,647 INFO : [ProcessWithActors] - First rowKey processed: dr0|urn:lsid:icmbio.gov.br:icmbio.parnaso.occurrence:MA120999 2014-05-20 14:15:05,998 INFO : [ProcessWithActors] - Last row key processed: dr0|urn:lsid:icmbio.gov.br:icmbio.parnaso.occurrence:MA99991 2014-05-20 14:15:06,006 INFO : [ProcessWithActors] - Finished. 2014-05-20 14:15:06,015 INFO : [AttributionDAO] - Calling web service for dr0 2014-05-20 14:15:06,017 INFO : [Consumer] - Killing (Actor.act) thread: 3 2014-05-20 14:15:06,016 INFO : [Consumer] - Killing (Actor.act) thread: 2 2014-05-20 14:15:06,015 INFO : [Consumer] - Killing (Actor.act) thread: 1 2014-05-20 14:15:06,289 INFO : [AttributionDAO] - Looking up collectory web service for ICMBIO|PARNASO May 20, 2014 2:15:10 PM org.geotools.referencing.factory.epsg.ThreadedEpsgFactory <init> INFO: Setting the EPSG factory org.geotools.referencing.factory.epsg.DefaultFactory to a 1800000ms timeout May 20, 2014 2:15:10 PM org.geotools.referencing.factory.epsg.ThreadedEpsgFactory <init> INFO: Setting the EPSG factory org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory to a 1800000ms timeout May 20, 2014 2:15:10 PM org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory createDataSource INFO: Building new data source for org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory May 20, 2014 2:15:10 PM org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory createBackingStore INFO: Building backing store for org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory 2014-05-20 14:15:32,105 INFO : [Consumer] - Killing (Actor.act) thread: 0 Indexing live with URL: null, and params: null&dataResource=dr0 java.lang.NullPointerException at au.org.ala.util.CMD$.au$org$ala$util$CMD$$indexDataResourceLive$1(CommandLineTool.scala:371) at au.org.ala.util.CMD$$anonfun$executeCommand$2.apply(CommandLineTool.scala:90) at au.org.ala.util.CMD$$anonfun$executeCommand$2.apply(CommandLineTool.scala:86) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:105) at au.org.ala.util.CMD$.executeCommand(CommandLineTool.scala:86) at au.org.ala.util.CommandLineTool$.main(CommandLineTool.scala:26) at au.org.ala.util.CommandLineTool.main(CommandLineTool.scala)
Nowadays we use the biocache-1.0-SNAPSHOT in our environment. But in your last mail you mentioned the version biocache-1.1-assembly.
I did download of this newer version, but when I ran it (ingest dr0) in our environment the system showed many errors (see below).
log4j:WARN custom level class [org.ala.client.appender.RestLevel] not found. Exception in thread "main" java.lang.ExceptionInInitializerError at au.org.ala.biocache.load.DataLoader$class.$init$(DataLoader.scala:28) at au.org.ala.biocache.load.Loader.<init>(Loader.scala:34) at au.org.ala.biocache.cmd.CMD$.executeCommand(CMD.scala:29) at au.org.ala.biocache.cmd.CommandLineTool$.main(CommandLineTool.scala:22) at au.org.ala.biocache.cmd.CommandLineTool.main(CommandLineTool.scala) Caused by: com.google.inject.CreationException: Guice creation errors:
1) No implementation for java.lang.Integer annotated with @com.google.inject.name.Named(value=cassandra.max.connections) was bound. while locating java.lang.Integer annotated with @com.google.inject.name.Named(value=cassandra.max.connections) for parameter 4 at au.org.ala.biocache.persistence.CassandraPersistenceManager.<init>(CassandraPersistenceManager.scala:24) at au.org.ala.biocache.ConfigModule.configure(Config.scala:184)
2) No implementation for java.lang.Integer annotated with @com.google.inject.name.Named(value=cassandra.max.retries) was bound. while locating java.lang.Integer annotated with @com.google.inject.name.Named(value=cassandra.max.retries) for parameter 5 at au.org.ala.biocache.persistence.CassandraPersistenceManager.<init>(CassandraPersistenceManager.scala:24) at au.org.ala.biocache.ConfigModule.configure(Config.scala:184)
3) No implementation for java.lang.Integer annotated with @com.google.inject.name.Named(value=cassandra.port) was bound. while locating java.lang.Integer annotated with @com.google.inject.name.Named(value=cassandra.port) for parameter 1 at au.org.ala.biocache.persistence.CassandraPersistenceManager.<init>(CassandraPersistenceManager.scala:24) at au.org.ala.biocache.ConfigModule.configure(Config.scala:184)
4) No implementation for java.lang.Integer annotated with @com.google.inject.name.Named(value=thrift.operation.timeout) was bound. while locating java.lang.Integer annotated with @com.google.inject.name.Named(value=thrift.operation.timeout) for parameter 6 at au.org.ala.biocache.persistence.CassandraPersistenceManager.<init>(CassandraPersistenceManager.scala:24) at au.org.ala.biocache.ConfigModule.configure(Config.scala:184)
5) No implementation for java.lang.String annotated with @com.google.inject.name.Named(value=cassandra.hosts) was bound. while locating java.lang.String annotated with @com.google.inject.name.Named(value=cassandra.hosts) for parameter 0 at au.org.ala.biocache.persistence.CassandraPersistenceManager.<init>(CassandraPersistenceManager.scala:24) at au.org.ala.biocache.ConfigModule.configure(Config.scala:184)
6) No implementation for java.lang.String annotated with @com.google.inject.name.Named(value=cassandra.keyspace) was bound. while locating java.lang.String annotated with @com.google.inject.name.Named(value=cassandra.keyspace) for parameter 3 at au.org.ala.biocache.persistence.CassandraPersistenceManager.<init>(CassandraPersistenceManager.scala:24) at au.org.ala.biocache.ConfigModule.configure(Config.scala:184)
7) No implementation for java.lang.String annotated with @com.google.inject.name.Named(value=cassandra.pool) was bound. while locating java.lang.String annotated with @com.google.inject.name.Named(value=cassandra.pool) for parameter 2 at au.org.ala.biocache.persistence.CassandraPersistenceManager.<init>(CassandraPersistenceManager.scala:24) at au.org.ala.biocache.ConfigModule.configure(Config.scala:184)
8) No implementation for java.lang.String annotated with @com.google.inject.name.Named(value=exclude.sensitive.values) was bound. while locating java.lang.String annotated with @com.google.inject.name.Named(value=exclude.sensitive.values) for parameter 1 at au.org.ala.biocache.index.SolrIndexDAO.<init>(SolrIndexDAO.scala:28) at au.org.ala.biocache.ConfigModule.configure(Config.scala:164)
9) No implementation for java.lang.String annotated with @com.google.inject.name.Named(value=extra.misc.fields) was bound. while locating java.lang.String annotated with @com.google.inject.name.Named(value=extra.misc.fields) for parameter 2 at au.org.ala.biocache.index.SolrIndexDAO.<init>(SolrIndexDAO.scala:28) at au.org.ala.biocache.ConfigModule.configure(Config.scala:164)
10) No implementation for java.lang.String annotated with @com.google.inject.name.Named(value=solr.home) was bound. while locating java.lang.String annotated with @com.google.inject.name.Named(value=solr.home) for parameter 0 at au.org.ala.biocache.index.SolrIndexDAO.<init>(SolrIndexDAO.scala:28) at au.org.ala.biocache.ConfigModule.configure(Config.scala:164)
10 errors at com.google.inject.internal.Errors.throwCreationExceptionIfErrorsExist(Errors.java:354) at com.google.inject.InjectorBuilder.initializeStatically(InjectorBuilder.java:152) at com.google.inject.InjectorBuilder.build(InjectorBuilder.java:105) at com.google.inject.Guice.createInjector(Guice.java:92) at com.google.inject.Guice.createInjector(Guice.java:69) at com.google.inject.Guice.createInjector(Guice.java:59) at au.org.ala.biocache.Config$.<init>(Config.scala:24) at au.org.ala.biocache.Config$.<clinit>(Config.scala) ... 5 more
Related to these specific issues (data update and incremental load), I will need to upgrade the biocache version (1.1 or newer) or I could work with the version 1.0-SNAPSHOT? If I update this version, I will have compatibility with the other components? How should I proceed?
Which layer files should I include in my environment to run these tests?
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
2014-05-09 2:14 GMT-03:00 <David.Martin@csiro.aumailto:David.Martin@csiro.au>: 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.commailto:daniel.lins@gmail.com] Sent: 09 May 2014 14:27
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
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
________________________________ 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.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
-- 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