March 2014 - ALA-Portal - lists.gbif.org

internationalization problems
by Suelane G. Fontes 09 Apr '14

09 Apr '14

3 9

Names Generator Issues
by Allan Koch 03 Apr '14

03 Apr '14

Does anyone knows where I can download this jar: *ala-names-generator-1.0-SNAPSHOT-assembly.jar*? I´m trying to generate a new Taxon Name List based on NSL for the Biocache processing. This instructions has been followed: http://code.google.com/p/ala-portal/wiki/UpgradeALANames According the instructions, I need to run this command: java -Xmx1G -Xms1G -cp .:ala-names-generator-1.0-SNAPSHOT-assembly.jar au.org.ala.names.NamesGenerator --all But, I can´t find this JAR. We are trying to build the Scala Project, but we are having some troubles. Would help me, for while, if I could run a ready JAR. Best regards, Allan Koch Veiga Research Center on Biodiversity and Computing - BioComp University of São Paulo Laboratório de Automação Agrícola - LAA Depto. de Engenharia de Computação e Sistemas Digitais - PCS Engenharia Elétrica - Escola Politécnica da USP Celular: +55 11 98401-2277 Email: allan.kv(a)usp.br "*Stay hungry, stay foolish.*" Stewart Brand

6 16

DwC-A Loading and Biocache Methods.
by Daniel Lins 25 Mar '14

25 Mar '14

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/b…) 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 <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 <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 <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 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 <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 <http://192.168.15.132:8080/collectory/ws/dataResource/dr4> | dr4 |* * | Teste 11 | http://192.168.15.132:8080/collectory/ws/dataResource/dr0 <http://192.168.15.132:8080/collectory/ws/dataResource/dr0> | dr0 |* * | Teste 12 | http://192.168.15.132:8080/collectory/ws/dataResource/dr3 <http://192.168.15.132:8080/collectory/ws/dataResource/dr3> | dr3 |* * | Teste 2 | http://192.168.15.132:8080/collectory/ws/dataResource/dr2 <http://192.168.15.132:8080/collectory/ws/dataResource/dr2> | dr2 |* * | Teste 3 | http://192.168.15.132:8080/collectory/ws/dataResource/dr1 <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 <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(a)usp.br daniel.lins(a)gmail.com

2 1

Internacionalization (i18n) of the Hubs module
by Suelane G. Fontes 20 Mar '14

20 Mar '14

2 1

Adding institution locations in the collectory module.
by Daniel Lins 19 Mar '14

19 Mar '14

Hello guys, I have a problem during the registry of institution locations (and collections) in collectory module. The system does not accept any geographical coordinates. All coordinates generated the same error before saving. For instance: Latitude: -35.307494965549076 Longitude: 149.10190973281863 Error message: "O campo [latitude] da classe [class au.org.ala.collectory.Institution] com o valor [-35.307.494.965.549.076] não atinge o valor mínimo [-360] O campo [longitude] da classe [class au.org.ala.collectory.Institution] como valor [14.910.190.973.281.863] ultrapass o valor máximo [360]" (translated) "The field [latitude] of class [class au.org.ala.collectory.Institution] with value [-3,530,469,319,052,836] does not reach the minimum value [-360]... " I also had that problem in the http://ala-demo.gbif.org. Someone had the same problem? Thanks. Regards, -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com

3 4

How to bypass the authentication process of Collectory component
by Daniel Lins 18 Mar '14

18 Mar '14

Hi Guys, We did the deployment of the main ALA components (Biocache, Hubs-webapp and Collectory) and now we do some tests with local data. However, we don't have access to the administrative features of Collectory component. We check that the ALA access control is accomplished through the CAS component (Central Authentication Service), and we will install it soon. Now we would like to bypass this authentication in order to test the administrative features without the CAS deployment/configuration. I noticed that exist some parameters in the collectory configuration files to do this, but in our tests did not work properly. Can we disable (bypass) the authentication process to use the collectory administrative features without the CAS deployment? How to do this? Thanks. Best Regards, -- Daniel Lins da Silva (Cel) 55 11 96144-4050 Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br daniel.lins(a)gmail.com

3 5

CentOS installation
by Tim Robertson [GBIF] 07 Mar '14

07 Mar '14

Hi all, Today I nearly finished porting the installation procedure to an Ansible [1] format, and I'm using CentOS. I've got a few little things to finish (like the Apache host definitions) but the apps are all running. Is anyone else using CentOS? Is anyone else using Ansible? If so, I'll spend the time to tidy this up a bit and offer it back to the ALA team, and open the discussion if Ansible would be a suitable format for deployment going forward - my personal impression is that is a good tool for this, and would allow easier and more flexible deployments. I am also using Vagrant [2] to bring up the virtual hosts on my laptop for testing. I could commit that back too, since it allows a complete working installation for testing with 2 commands: $ vagrant up $ ansible-playbook -i vagrant site.yml --private-key /Users/tim/.ssh/id_dsa I'd be interested in hearing how others are doing. I've run in to a few niggly issues, but mainly because I am deviating from the procedure, in order to understand it better. Thanks all, Tim [1] http://www.ansible.com/home [2] http://www.vagrantup.com/ ---------------------------------------------------------------------------------------- Tim Robertson - GBIF Head of Informatics - trobertson(a)gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark Tel: +45 3532 1487 Mob: +45 2826 1487 Fax: +45 2875 1480 ----------------------------------------------------------------------------------------

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