Hi guys,

I am having troubles to load DwC-A files in Biocache store. The error occurs during the archive loading (The error message is shown below).

$ sudo java -cp .:biocache.jar au.org.ala.util.DwCALoader dr3 -l dwca-teste3.zip

2014-03-25 02:40:50,769 INFO : [ConfigModule] - Loading configuration from /data/biocache/config/biocache-config.properties

2014-03-25 02:40:51,031 INFO : [ConfigModule] - Initialise SOLR

2014-03-25 02:40:51,035 INFO : [ConfigModule] - Initialise name matching indexes

2014-03-25 02:40:51,539 INFO : [ConfigModule] - Initialise persistence manager

2014-03-25 02:40:51,541 INFO : [ConfigModule] - Configure complete

Loading archive dwca-teste3.zip for resource dr3 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)

I used a DwC-A file with comma delimiter and another file with tab delimiter. But both files generated the same error.

During the tests, I replaced the biocache.jar file from the other .jar file sent by Natasha in a previous email (http://maven.ala.org.au/repository/au/org/ala/biocache-store/1.0-SNAPSHOT/biocache-store-1.0-SNAPSHOT-assembly.jar) but I had the same problem.

I also verified that list() and describe() methods of the Biocache are producing some errors too.

These problems may be related to the registryURL property. When registryURL= http://192.168.15.132:8080/collectory, I have the errors below:

biocache> list

2014-03-25 03:09:24,305 INFO : [ConfigModule] - Loading configuration from /data/biocache/config/biocache-config.properties

2014-03-25 03:09:24,586 INFO : [ConfigModule] - Initialise SOLR

2014-03-25 03:09:24,591 INFO : [ConfigModule] - Initialise name matching indexes

2014-03-25 03:09:25,133 INFO : [ConfigModule] - Initialise persistence manager

2014-03-25 03:09:25,143 INFO : [ConfigModule] - Configure complete

java.net.ConnectException: Connection refused

at java.net.PlainSocketImpl.socketConnect(Native Method)

at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)

at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)

at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)

at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)

at java.net.Socket.connect(Socket.java:579)

at java.net.Socket.connect(Socket.java:528)

at sun.net.NetworkClient.doConnect(NetworkClient.java:180)

at sun.net.www.http.HttpClient.openServer(HttpClient.java:432)

at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)

at sun.net.www.http.HttpClient.<init>(HttpClient.java:211)

at sun.net.www.http.HttpClient.New(HttpClient.java:308)

at sun.net.www.http.HttpClient.New(HttpClient.java:326)

at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:996)

at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:932)

at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:850)

at sun.net.www.protocol.http.HttpURLConnection.followRedirect(HttpURLConnection.java:2398)

at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1557)

at java.net.URL.openStream(URL.java:1037)

at scala.io.Source$.fromURL(Source.scala:140)

at scala.io.Source$.fromURL(Source.scala:130)

at au.org.ala.util.Loader.printResourceList(Loader.scala:52)

at au.org.ala.util.CMD$.executeCommand(CommandLineTool.scala:78)

at au.org.ala.util.CommandLineTool$.main(CommandLineTool.scala:26)

at au.org.ala.util.CommandLineTool.main(CommandLineTool.scala)

biocache> describe dr3

UID: dr3

This data resource was last checked None

Protocol: DwCA

URL: http://192.168.15.132:8080/collectory/upload/1395634757631/dwca-teste3.zip

Unique terms: occurrenceID

url: http://192.168.15.132:8080/collectory/upload/1395634757631/dwca-teste3.zip

java.lang.ClassCastException: java.lang.Boolean cannot be cast to java.lang.String

at au.org.ala.util.Loader$$anonfun$describeResource$1$$anonfun$apply$1.apply(Loader.scala:45)

at scala.collection.immutable.HashMap$HashMap1.foreach(HashMap.scala:224)

at scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:403)

at au.org.ala.util.Loader$$anonfun$describeResource$1.apply(Loader.scala:45)

at au.org.ala.util.Loader$$anonfun$describeResource$1.apply(Loader.scala:38)

at scala.collection.immutable.List.foreach(List.scala:309)

at au.org.ala.util.Loader.describeResource(Loader.scala:38)

at au.org.ala.util.CMD$.executeCommand(CommandLineTool.scala:77)

at au.org.ala.util.CommandLineTool$.main(CommandLineTool.scala:26)

at au.org.ala.util.CommandLineTool.main(CommandLineTool.scala)

When registryURL= http://192.168.15.132:8080/collectory/ws, I have the below errors :

biocache> list

2014-03-25 03:22:52,278 INFO : [ConfigModule] - Loading configuration from /data/biocache/config/biocache-config.properties

2014-03-25 03:22:52,526 INFO : [ConfigModule] - Initialise SOLR

2014-03-25 03:22:52,531 INFO : [ConfigModule] - Initialise name matching indexes

2014-03-25 03:22:53,051 INFO : [ConfigModule] - Initialise persistence manager

2014-03-25 03:22:53,060 INFO : [ConfigModule] - Configure complete

-----------------------------------------------------------------------------------------------------------------------

| name | uri | uid |

|---------------------------------------------------------------------------------------------------------------------|

| Teste 10 | http://192.168.15.132:8080/collectory/ws/dataResource/dr4 | dr4 |

| Teste 11 | http://192.168.15.132:8080/collectory/ws/dataResource/dr0 | dr0 |

| Teste 12 | http://192.168.15.132:8080/collectory/ws/dataResource/dr3 | dr3 |

| Teste 2 | http://192.168.15.132:8080/collectory/ws/dataResource/dr2 | dr2 |

| Teste 3 | http://192.168.15.132:8080/collectory/ws/dataResource/dr1 | dr1 |

-----------------------------------------------------------------------------------------------------------------------

biocache> describe dr3

java.io.FileNotFoundException: http://192.168.15.132:8080/collectory/ws/ws/dataResource/dr3.json

at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1624)

at java.net.URL.openStream(URL.java:1037)

at scala.io.Source$.fromURL(Source.scala:140)

at scala.io.Source$.fromURL(Source.scala:130)

at au.org.ala.biocache.DataLoader$class.getDataResourceDetailsAsMap(dataimport.scala:99)

at au.org.ala.util.Loader.getDataResourceDetailsAsMap(Loader.scala:31)

at au.org.ala.biocache.DataLoader$class.retrieveConnectionParameters(dataimport.scala:116)

at au.org.ala.util.Loader.retrieveConnectionParameters(Loader.scala:31)

at au.org.ala.util.Loader$$anonfun$describeResource$1.apply(Loader.scala:39)

at au.org.ala.util.Loader$$anonfun$describeResource$1.apply(Loader.scala:38)

at scala.collection.immutable.List.foreach(List.scala:309)

at au.org.ala.util.Loader.describeResource(Loader.scala:38)

at au.org.ala.util.CMD$.executeCommand(CommandLineTool.scala:77)

at au.org.ala.util.CommandLineTool$.main(CommandLineTool.scala:26)

at au.org.ala.util.CommandLineTool.main(CommandLineTool.scala)

How could I do the loading of DwC-A files? These problems are related?

Thanks!

Cheers,

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