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

Issue to view occurrence images on the Hubs.
by Daniel Lins 27 Jun '14

27 Jun '14

Hi Dave, After I updated the biocache-service to the version 1.1, I stopped viewing the occurrence images in the hubs portal. All images urls were set to http://biocache.ala.org.au/biocache-media. e.g. http://biocache.ala.org.au/biocache-media/dr0/20750/8fe44933-7970-4b3e-a2d8… Maybe it's a issue, because in the biocache-service code (tags/biocache-service-1.1/src/main/java/au/org/ala/biocache/dto/OccurrenceIndex.java) the application is not checking the external configuration file. It is looking to "/biocache.properties". This file does not exist in this folder, thus the application always uses the default media url (" http://biocache.ala.org.au/biocache-media/"), generating this error. public class OccurrenceIndex { public static String biocacheMediaUrl = " http://biocache.ala.org.au/biocache-media/"; public static String biocacheMediaDir = "/data/biocache-media/"; protected static final Logger logger = Logger.getLogger(OccurrenceIndex. class); static { //check the properties file for an override try { Properties p = new Properties(); p.load(OccurrenceIndex.class.getResourceAsStream( "/biocache.properties")); //InputStream inStream = Thread.currentThread().getContextClassLoader().getResourceAsStream("biocache.properties"); //p.load(inStream); logger.debug("Retrieved biocacheMediaUrl: " + p.getProperty( "biocacheMediaUrl")); logger.debug("Retrieved biocacheMediaDir: " + p.getProperty( "biocacheMediaDir")); if(p.getProperty("biocacheMediaUrl") != null) biocacheMediaUrl = p.getProperty("biocacheMediaUrl"); if(p.getProperty("biocacheMediaDir") != null) biocacheMediaDir = p.getProperty("biocacheMediaDir"); I changed this code to check first the property of the external configuration file ("/data/biocache/config/biocache-config.properties") and the visualization of images worked again. Regards, Daniel Lins da Silva (Mobile) 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

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Re: [Ala-portal] DwC-A loading problems
by David.Martin＠csiro.au 27 Jun '14

27 Jun '14

Thanks for resending Pedro. We are recommending using the Ansible scripts [1] for installation of components. If this isn't possible, its worth checking out the templates in use by these scripts [2]. There is a property at the bottom of this file that disables the API key check. security.apikey.checkEnabled=false That said, that error looks like a network issue between the machine that is running the collectory and the machine you are loading the data to. It's worth checking to see if the ports are open between these machines. Cheers Dave [1] https://github.com/gbif/ala-install<https://github.com/gbif/ala-install/blob/master/ansible/roles/collectory/te…> [2] https://github.com/gbif/ala-install/blob/master/ansible/roles/collectory/te… ________________________________ From: Daniel Lins [daniel.lins(a)gmail.com] Sent: 27 June 2014 13:54 To: Martin, Dave (CES, Black Mountain) Cc: ala-portal(a)lists.gbif.org; Pedro Corrêa Subject: Re: [Ala-portal] DwC-A loading problems Hi Dave, Did you see this mail? Do you think this issue can be something related to the configuration of api_key property? Thanks. Regards, 2014-06-25 2:14 GMT-03:00 Daniel Lins <daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com>>: Hi Dave, Thanks for the support. The data loading in the biocache is working properly now. But error continues during the update of collectory (see below). java.net.SocketTimeoutException: Read timed out at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:526) at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1675) at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1673) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1671) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1244) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468) at scalaj.http.Http$Request.liftedTree1$1(Http.scala:107) at scalaj.http.Http$Request.process(Http.scala:103) at scalaj.http.Http$Request.responseCode(Http.scala:120) at au.org.ala.biocache.load.DataLoader$class.updateLastChecked(DataLoader.scala:354) at au.org.ala.biocache.load.DwCALoader.updateLastChecked(DwCALoader.scala:74) at au.org.ala.biocache.load.DwCALoader.load(DwCALoader.scala:103) at au.org.ala.biocache.load.Loader.load(Loader.scala:75) at au.org.ala.biocache.cmd.CMD$$anonfun$executeCommand$7.apply(CMD.scala:69) at au.org.ala.biocache.cmd.CMD$$anonfun$executeCommand$7.apply(CMD.scala:69) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108) at au.org.ala.biocache.cmd.CMD$.executeCommand(CMD.scala:69) at au.org.ala.biocache.cmd.CommandLineTool$.main(CommandLineTool.scala:22) at au.org.ala.biocache.cmd.CommandLineTool.main(CommandLineTool.scala) Caused by: java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:152) at java.net.SocketInputStream.read(SocketInputStream.java:122) at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) at java.io.BufferedInputStream.read(BufferedInputStream.java:334) at sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:687) at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:633) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1323) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468) at scalaj.http.Http$Request$$anonfun$responseCode$1.apply(Http.scala:120) atscala j.http.Http$Request$$anonfun$responseCode$1.apply(Http.scala:120) at scalaj.http.Http$Request.liftedTree1$1(Http.scala:104) ... 13 more In the external configuration file (/data/biocache/config/biocache-config.properties) the property registry.url is correct (registry.url=http://192.168.15.132:8080/<http://192.168.15.132:8080/>collectory/ws), indicating the URL of the collectory WS page. It could be something related to permission for external access? How works this api_key property in the collectory? Thanks! Regards, Daniel Lins da Silva (Mobile) 55 11 96144-4050<tel:55%2011%2096144-4050> Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> 2014-06-20 2:26 GMT-03:00 <David.Martin(a)csiro.au<mailto:David.Martin@csiro.au>>: Hi Daniel. There is a version updated of biocache-store of 1.1.1 that helped fix some of the problems Burke spotted when loading darwin core archives downloaded from the GBIF portal. The symptom where similar (only one record loaded for a dataset). The exception in point 3) indicates the URL you have configured for the collectory (registry.url in biocache.properties) is either incorrect, or the collectory can not be accessed for some reason. At the end of data load, the collectory is updated to indicate the last loaded date for that dataset. This is done using a webservice. One thing to mention - if you want to remove all data from your database, the easiest thing to do is use the cassandra-cli and run the command: >> truncate occ; This will remove all occurrence records from the database, but not from the index. The warnings you are seeing in the processing phase e.g. 2014-06-20 01:51:20,505 WARN : [ALANameSearcher] - Unable to parse Abaca bunchy top (Babuvirus). Name of type virus unparsable: Abaca bunchy top (Babuvirus) are normal. This is referring to the sensitive species list in use. Cheers Dave ________________________________ From: Daniel Lins [daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com>] Sent: 20 June 2014 15:11 To: Martin, Dave (CES, Black Mountain) Cc: ala-portal(a)lists.gbif.org<mailto:ala-portal@lists.gbif.org>; dos Remedios, Nick (CES, Black Mountain); Pedro Corrêa Subject: Re: [Ala-portal] DwC-A loading problems Hi Dave, thanks for the information from the last email. I'm following your advice and performing the update of our test environment for biocache version 1.1. But I'm having some problems and I would like to know if you or anyone has already found this issue and know a solution. To update the biocache version I did these steps below (based on the Vagrant/Ansible installation process): 1. Cleaning of the database and index through delete-resource function (delete-resource dr0 dr1 dr2 ...); 2. An update of the Biocache config file (/data/biocache/config/biocache-config.properties) (copied from the Vagrant VM, with some configuration changes); 3. An update of the biocache build file (biocache. jar) (copied from the Vagrant VM - /usr/lib/biocache); 4. Deployment of the new biocache-service build (copied from the Vagrant VM - tomcat7/webapps/biocache-service.war) 5. An update of the Solr config files (schema.xml, solrconfig.xml) (copied from the Vagrant VM - /data/solr/biocache); 6. Exclusion of the indexing folder of Biocache Core (/data/solr/biocache/data); Notes 1 ** No change was made in the Hubs-Webapp and Collectory. Notes 2 ** The import of CSV files is working (using load-local-csv dr0 /<file_location>/xxx.csv). I tried to import a Darwin Core Archive by following these steps: 1. Created a data resource (dr0); 2. Uploaded a DWC-A zip file into the DR using the "Upload File" option. Protocol:DarwinCore archive Location URL:file:////data/collectory/upload/1403239521145/dwca-ocorrencias_lobo_guara_1.zip Automatically loaded:false DwC terms that uniquely identify a record: occurrenceID Strip whitespaces in key: false Incremental Load: false 3. Used the Command Line Tool (Biocache) to Load (load dr0), Process (process dr0) and Index (index dr0) data. During the data loading phase, the system generated these errors: ... 2014-06-20 01:49:12,506 INFO : [DataLoader] - Finished DwC loader. Records processed: 32 java.net.SocketTimeoutException: Read timed out at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:526) at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1675) at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1673) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1671) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1244) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468) at scalaj.http.Http$Request.liftedTree1$1(Http.scala:107) at scalaj.http.Http$Request.process(Http.scala:103) at scalaj.http.Http$Request.responseCode(Http.scala:120) at au.org.ala.biocache.load.DataLoader$class.updateLastChecked(DataLoader.scala:354) at au.org.ala.biocache.load.DwCALoader.updateLastChecked(DwCALoader.scala:74) at au.org.ala.biocache.load.DwCALoader.load(DwCALoader.scala:103) at au.org.ala.biocache.load.Loader.load(Loader.scala:75) at au.org.ala.biocache.cmd.CMD$$anonfun$executeCommand$7.apply(CMD.scala:69) at au.org.ala.biocache.cmd.CMD$$anonfun$executeCommand$7.apply(CMD.scala:69) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108) at au.org.ala.biocache.cmd.CMD$.executeCommand(CMD.scala:69) at au.org.ala.biocache.cmd.CommandLineTool$.main(CommandLineTool.scala:22) at au.org.ala.biocache.cmd.CommandLineTool.main(CommandLineTool.scala) Caused by: java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:152) at java.net.SocketInputStream.read(SocketInputStream.java:122) at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) at java.io.BufferedInputStream.read(BufferedInputStream.java:334) at sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:687) at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:633) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1323) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468) at scalaj.http.Http$Request$$anonfun$responseCode$1.apply(Http.scala:120) at scalaj.http.Http$Request$$anonfun$responseCode$1.apply(Http.scala:120) at scalaj.http.Http$Request.liftedTree1$1(Http.scala:104) ... 13 more And in Cassandra was saved only one record: cqlsh:occ> select * from occ; key | portalId | uuid ----------+----------+-------------------------------------- dr0|null | null | 1b5b21fc-594a-46e6-b8db-cf37c50b8f7b During the data processing phase, the system generated these additional errors: ... Jun 20, 2014 1:51:08 AM org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory createDataSource INFO: Building new data source for org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory Jun 20, 2014 1:51:08 AM org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory createBackingStore INFO: Building backing store for org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory 2014-06-20 01:51:20,505 WARN : [ALANameSearcher] - Unable to parse Abaca bunchy top (Babuvirus). Name of type virus unparsable: Abaca bunchy top (Babuvirus) 2014-06-20 01:51:20,509 WARN : [ALANameSearcher] - Unable to parse Abaca mosaic, sugarcane mosaic (Potyvirus). Name of type virus unparsable: Abaca mosaic, sugarcane mosaic (Potyvirus) 2014-06-20 01:51:21,210 WARN : [ALANameSearcher] - Unable to parse Acute bee paralysis (Cripavirus). Name of type virus unparsable: Acute bee paralysis (Cripavirus) 2014-06-20 01:51:21,255 WARN : [ALANameSearcher] - Unable to parse Agropyron mosaic (Rymovirus). Name of type virus unparsable: Agropyron mosaic (Rymovirus) 2014-06-20 01:51:21,289 WARN : [ALANameSearcher] - Unable to parse Alphacrytovirus vicia. Name of type virus unparsable: Alphacrytovirus vicia 2014-06-20 01:51:21,334 WARN : [ALANameSearcher] - Unable to parse American plum line pattern (APLPV, Ilaravirus). Name of type virus unparsable: American plum line pattern (APLPV, Ilaravirus) 2014-06-20 01:51:21,525 WARN : [ALANameSearcher] - Unable to parse Apis iridescent (Iridovirus). Name of type virus unparsable: Apis iridescent (Iridovirus) 2014-06-20 01:51:21,546 WARN : [ALANameSearcher] - Unable to parse Apricot ring pox (Unassigned). Name of type blacklisted unparsable: Apricot ring pox (Unassigned) 2014-06-20 01:51:21,549 WARN : [ALANameSearcher] - Unable to parse Arabis mosaic (Nepovirus). Name of type virus unparsable: Arabis mosaic (Nepovirus) 2014-06-20 01:51:21,623 WARN : [ALANameSearcher] - Unable to parse Artichoke Italian latent (Nepovirus). Name of type virus unparsable: Artichoke Italian latent (Nepovirus) 2014-06-20 01:51:21,640 WARN : [ALANameSearcher] - Unable to parse Asparagus (Ilarvirus). Name of type virus unparsable: Asparagus (Ilarvirus) 2014-06-20 01:51:21,641 WARN : [ALANameSearcher] - Unable to parse Asparagus (Potyvirus). Name of type virus unparsable: Asparagus (Potyvirus) ... During the last phase there were no errors. However, only one record was indexed. 2014-06-20 01:54:07,739 INFO : [SolrIndexDAO] - >>>>>>>>>>>>> Document count of index: 1 2014-06-20 01:54:07,741 INFO : [SolrIndexDAO] - Finalise finished. I attached a file with the complete messages generated by Biocache during this test. Thanks! Cheers. Daniel Lins da Silva (Mobile) 55 11 96144-4050<tel:55%2011%2096144-4050> Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> 2014-06-18 6:15 GMT-03:00 <David.Martin(a)csiro.au<mailto:David.Martin@csiro.au>>: 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(a)gmail.com<mailto:daniel.lins@gmail.com>] Sent: 18 June 2014 15:54 To: Martin, Dave (CES, Black Mountain) Cc: ala-portal(a)lists.gbif.org<mailto: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 96144-4050<tel:55%2011%2096144-4050> Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> 2014-05-26 3:58 GMT-03:00 <David.Martin(a)csiro.au<mailto: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-serv… Cheers Dave Martin ALA ________________________________ From: Daniel Lins [daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com>] Sent: 26 May 2014 15:02 To: Martin, Dave (CES, Black Mountain) Cc: ala-portal(a)lists.gbif.org<mailto: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 96144-4050<tel:55%2011%2096144-4050> Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> 2014-05-09 2:14 GMT-03:00 <David.Martin(a)csiro.au<mailto: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(a)gmail.com<mailto:daniel.lins@gmail.com>] Sent: 09 May 2014 14:27 To: Martin, Dave (CES, Black Mountain) Cc: ala-portal(a)lists.gbif.org<mailto: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(a)csiro.au<mailto: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(a)gmail.com<mailto:daniel.lins@gmail.com>] Sent: 09 May 2014 13:59 To: Martin, Dave (CES, Black Mountain) Cc: ala-portal(a)lists.gbif.org<mailto: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 96144-4050<tel:55%2011%2096144-4050> Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> 2014-05-07 0:46 GMT-03:00 <David.Martin(a)csiro.au<mailto: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(a)gmail.com<mailto:daniel.lins@gmail.com>] Sent: 05 May 2014 15:39 To: Quimby, Natasha (CES, Black Mountain) Cc: ala-portal(a)lists.gbif.org<mailto: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 96144-4050<tel:55%2011%2096144-4050> Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> 2014-04-28 3:52 GMT-03:00 Daniel Lins <daniel.lins(a)gmail.com<mailto: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<tel:55%2011%2096144-4050> Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> 2014-04-28 3:26 GMT-03:00 <Natasha.Quimby(a)csiro.au<mailto: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(a)gmail.com<mailto:daniel.lins@gmail.com>> Date: Monday, 28 April 2014 3:54 PM To: "ala-portal(a)lists.gbif.org<mailto:ala-portal@lists.gbif.org>" <ala-portal(a)lists.gbif.org<mailto:ala-portal@lists.gbif.org><mailto:ala-portal@lists.gbif.org><mailto:ala-portal@lists.gbif.org><mailto:ala-portal@lists.gbif.org><mailto:ala-portal@lists.gbif.org><mailto:ala-portal@lists.gbif.org><mailto:ala-portal@lists.gbif.org>>, "dos Remedios, Nick (CES, Black Mountain)" <Nick.Dosremedios(a)csiro.au<mailto:Nick.Dosremedios@csiro.au>>, "Martin, Dave (CES, Black Mountain)" <David.Martin(a)csiro.au<mailto: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 96144-4050<tel:55%2011%2096144-4050> Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> -- Daniel Lins da Silva (Cel) 11 6144-4050 daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com>

2 1

DwC-A loading problems
by Daniel Lins 27 Jun '14

27 Jun '14

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(a)usp.br daniel.lins(a)gmail.com

3 18

Using Biocache-Store and Apache Cassandra on different servers
by Daniel Lins 27 Jun '14

27 Jun '14

Hi, We configured the ALA applications on different Servers of the database Server. However, we are having problems running the biocache-store. I changed the biocache configuration file (/data/biocache/config/biocache-config.properties) and the Cassandra configuration (cassandra.yaml) for enabling remote access. (biocache-config.properties) # Cassandra Config db=cassandra *cassandra.hosts=192.168.15.199* cassandra.port=9160 cassandra.pool=biocache-store-pool cassandra.keyspace=occ cassandra.max.connections=-1 cassandra.max.retries=6 thrift.operation.timeout=8000 (cassandra.yaml) *listen_address: 192.168.15.199* *rpc_address: 192.168.15.199* *rpc_port: 9160* ... *Running the Biocache-store in the server 192.168.15.132* When I ran the Loading method, the data were saved correctly in the Cassandra Database. However, in the Processing method, the data was not recovered (see message below) and the Indexing method did not index. biocache> process dr0 Processing dr0 incremental=false 2014-06-25 00:17:20,228 INFO : [Consumer] - Initialising thread: 0 2014-06-25 00:17:20,270 INFO : [Consumer] - Initialising thread: 1 2014-06-25 00:17:20,271 INFO : [Consumer] - Initialising thread: 2 2014-06-25 00:17:20,274 INFO : [Consumer] - Initialising thread: 3 2014-06-25 00:17:20,275 INFO : [ProcessWithActors] - Starting with dr0| endingwith dr0|~ 2014-06-25 00:17:20,275 INFO : [ProcessWithActors] - Initialised actors... 2014-06-25 00:17:20,274 INFO : [Consumer] - In thread: 0 2014-06-25 00:17:20,274 INFO : [Consumer] - In thread: 1 2014-06-25 00:17:20,281 INFO : [Consumer] - In thread: 2 2014-06-25 00:17:20,293 INFO : [Consumer] - In thread: 3 2014-06-25 00:17:20,326 INFO : [ProcessWithActors] - Last row key processed: 2014-06-25 00:17:20,327 INFO : [ProcessWithActors] - Finished. 2014-06-25 00:17:20,333 INFO : [Consumer] - Killing (Actor.act) thread: 0 2014-06-25 00:17:20,333 INFO : [Consumer] - Killing (Actor.act) thread: 3 2014-06-25 00:17:20,333 INFO : [Consumer] - Killing (Actor.act) thread: 2 2014-06-25 00:17:20,333 INFO : [Consumer] - Killing (Actor.act) thread: 1 biocache> index dr0 2014-06-25 00:17:36,848 INFO : [IndexRecords] - Starting to index dr0| until dr0|~ 2014-06-25 00:17:36,858 INFO : [IndexRecords] - Total indexing time 0.005 seconds 2014-06-25 00:17:36,858 INFO : [SolrIndexDAO] - Initialising the solr server http://192.168.15.132:8080/solr null null 2014-06-25 00:17:36,859 INFO : [SolrIndexDAO] - Initialising connection to SOLR server..... 2014-06-25 00:17:37,764 INFO : [SolrIndexDAO] - Initialising connection to SOLR server - done. 2014-06-25 00:17:38,040 INFO : [SolrIndexDAO] - >>>>>>>>>>>>> Document count of index: 0 2014-06-25 00:17:38,041 INFO : [SolrIndexDAO] - Finalise finished. ** The delete_resource method also didn't work and I need to delete the occurrence table using the truncate command. Does anyone know how to solve this issue? Thanks!! Regards, -- Daniel Lins da Silva (Mobile) 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

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Ingest problem :(
by Santiago Martinez de la Riva 26 Jun '14

26 Jun '14

Hi Dave, I'm checking out the ansible script, and I have a problem with the field mapping in the indexing process. The question is that when I upload this resource http://api.gbif.org/v0.9/occurrence/download/request/0000874-14061609374922… ( http://www.gbif.org/dataset/835177da-f762-11e1-a439-00145eb45e9a) and I try to ingest the records. The mapping that the process applies for the indexing, it's wrong. (Look attach image please) It's like if one column is moved one position left. The begining of this problem appears in the column: <field index="54" term="http://purl.org/dc/terms/type"/> The next columns are moved one position left. It's weird. For this reason, you can see that the field "Associated taxa" is "Basis of record", and the same with the rest of the fields Could be a error in the internal map? In the meta.xml the order of the fields is right. I was thinking that it could be a error in the internal process of indexing Do you know what could be the problem?? Does anyone have the same problem as me?? Thanks so much. Kind Regards. --------------------------------------------------------------------------------------- Santiago Martínez de la Riva GBIF.ES, Unidad de Coordinación Tel. +34 91 4203017 x 273 Real Jardín Botánico - CSIC Fax +34 91 429 2405 Plaza de Murillo, 2 sama(a)gbif.es 28014 Madrid, Spain www.gbif.es

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getting started issues
by Miguel Carboni 24 Jun '14

24 Jun '14

Hi! I'm following the getting started page from: https://code.google.com/p/ala-portal/wiki/GettingStarted And had a couple of minor issues: - When I try to download cassandra and solr, the cited releases aren't available in mirror sites. I've downloaded this ones: http://apache.dattatec.com/cassandra/1.2.16/apache-cassandra-1.2.16-bin.tar… http://apache.dattatec.com/lucene/solr/4.8.1/solr-4.8.1.tgz I also had a little issue "unzip" the taxon.tgz. It looks like if it weren't zipped, just tared. $ tar xf taxon.tgz Will do. For the biocache service, the http://ala-portal.googlecode.com/svn/trunk/biocache-service/biocache-config… download link was broken. Is this a valid one? http://ala-portal.googlecode.com/svn/trunk/biocache-service/config/applicat… Is this properties file correct? http://ala-portal.googlecode.com/svn/trunk/biocache-service/config/biocache… I've found many references to remote servers. I've already changed the solrHome. Should I change any other? When I get to the biocache cli. If i press Enter or call any command I get $ java -cp .:biocache.jar -Xmx2g -Xms2g au.org.ala.util.CommandLineTool ---------------------------- | Biocache management tool | ---------------------------- Please supply a command or hit ENTER to view command list. biocache> healthcheck BANG! Guice exceptions! The full exception is in the attached file. Any clue? Is there any jar missing in the classpath or any configuration file missing? Thank you very much in advance and best regards, Miguel

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Re: [Ala-portal] Proposed workshop in Canberra 21-July - 25th July 2014
by David.Martin＠csiro.au 17 Jun '14

17 Jun '14

Hello all, We have had positive responses from projects in Brazil, France, Spain, Costa Rica and GBIF secretariat in Denmark. We plan to go ahead with the workshop in ALA offices, Canberra 21-25th July 2014. Below are two links to recommended accommodation in Canberra. Both of these options are within walking distance of the ALA offices. 1) Liversidge Apartments - http://accom.anu.edu.au/UAS/189.html 2) University House - http://www.anu.edu.au/unihouse/accomm/accommodation.html The ALA is happy to make accommodation bookings at these places on your behalf. We can not offer to cover the costs of the accommodation. Please send any booking requests to Heather Walsh (cc-ed). We will send out more details including an agenda & schedule in the next couple of weeks. Many thanks from the ALA team. Dave Martin ALA [1] Route from Liversidge Apartments to ALA offices https://goo.gl/maps/NIUyM [2] Route from University House to ALA offices https://goo.gl/maps/BhYvk 2014-06-11 22:38 GMT-06:00 <David.Martin(a)csiro.au<mailto:David.Martin@csiro.au>>: Dear all, Thanks for the early responses. At the moment we have expressions of interest from: GBIF: Tim and Burke Costa Rica: ? Sao Paulo: 2-3 people France: tentative 1 person? In discussion with GBIF (Tim R) we believe that this would be enough to make some good progress. Can I please ask that we have a confirmation by the 17th June of a commitment to attend? With this, we will begin arranging the workshop and logistics, and people can book flights etc. (GBIF (TR and BK) have confirmed attendance should this proceed) Cheers, Dave Martin ALA ________________________________ From: Martin, Dave (CES, Black Mountain) Sent: 06 June 2014 15:15 To: ala-portal(a)lists.gbif.org<mailto:ala-portal@lists.gbif.org> Cc: support(a)ala.org.au<mailto:support@ala.org.au>; Walsh, Heather (CES, Black Mountain); La Salle, John (CES, Black Mountain) Subject: Proposed workshop in Canberra - July 2014 Hello all, There have been a couple of approaches to the team at ALA asking for the possibility of a visit to help advance understanding of the system. Additionally we hear early indications of interest from the recent group who had a small workshop in Europe, but note their requests for improved documentation, processes and structure. It is short notice but we would like to propose a workshop in Canbera for developers on the week of : 21-July - 25th July 2014 During this week we would aim to: a) exchange knowledge amongst developers b) collate wiki documentation on data management, and customization of the web portal c) discuss and make progress in the processes surrounding source code management - e.g. potentially moving to Github and defining procedures for contribution, and releases Please note that at this stage and for the foreseeable future, we believe the components suitable for collaboration and adoption are: i. The biocache-hub webapp ii. The collectory webapp iii. The biocache backend processes I understand that the GBIF secretariat will commit to managing the key pieces of documentation and assist in helping structure the project. The ALA development team are committed to maintaining this codebase and using it to support applications in Australia. We don't envisage this being an off the shelf product such as the GBIF IPT, but rather a well managed open source project that people can contribute to and use as a framework to rapidly kick start their own developments. If you have interest in joining, could you please reply to this expressing interest, even if only tentative? Many thanks, Dave Martin ALA

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Re: [Ala-portal] Proposed workshop in Canberra 21-July - 25th July 2014
by David.Martin＠csiro.au 13 Jun '14

13 Jun '14

Dear all, Thanks for the early responses. At the moment we have expressions of interest from: GBIF: Tim and Burke Costa Rica: ? Sao Paulo: 2-3 people France: tentative 1 person? In discussion with GBIF (Tim R) we believe that this would be enough to make some good progress. Can I please ask that we have a confirmation by the 17th June of a commitment to attend? With this, we will begin arranging the workshop and logistics, and people can book flights etc. (GBIF (TR and BK) have confirmed attendance should this proceed) Cheers, Dave Martin ALA ________________________________ From: Martin, Dave (CES, Black Mountain) Sent: 06 June 2014 15:15 To: ala-portal(a)lists.gbif.org Cc: support(a)ala.org.au; Walsh, Heather (CES, Black Mountain); La Salle, John (CES, Black Mountain) Subject: Proposed workshop in Canberra - July 2014 Hello all, There have been a couple of approaches to the team at ALA asking for the possibility of a visit to help advance understanding of the system. Additionally we hear early indications of interest from the recent group who had a small workshop in Europe, but note their requests for improved documentation, processes and structure. It is short notice but we would like to propose a workshop in Canbera for developers on the week of : 21-July - 25th July 2014 During this week we would aim to: a) exchange knowledge amongst developers b) collate wiki documentation on data management, and customization of the web portal c) discuss and make progress in the processes surrounding source code management - e.g. potentially moving to Github and defining procedures for contribution, and releases Please note that at this stage and for the foreseeable future, we believe the components suitable for collaboration and adoption are: i. The biocache-hub webapp ii. The collectory webapp iii. The biocache backend processes I understand that the GBIF secretariat will commit to managing the key pieces of documentation and assist in helping structure the project. The ALA development team are committed to maintaining this codebase and using it to support applications in Australia. We don't envisage this being an off the shelf product such as the GBIF IPT, but rather a well managed open source project that people can contribute to and use as a framework to rapidly kick start their own developments. If you have interest in joining, could you please reply to this expressing interest, even if only tentative? Many thanks, Dave Martin ALA

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Update on the ALA "occurrence search" front-end system
by Nick.Dosremedios＠csiro.au 13 Jun '14

13 Jun '14

I’m writing this email to provide some background and clarification about the ALA occurrence search (front-end) web application. There are actually 2 separate versions of this web app. The old Spring MVC version which was developed over 3 years ago and a new Grails version which was developed this year. The demo site<http://ala-demo.gbif.org/> and ansible script<https://github.com/gbif/ala-install> both use the new Grails version. For those of you who have only used the ansible script, you can probably stop reading now. But for those people/groups who attended the workshop in Costa Rica last year, please read on… The new biocache-hubs Grails webapp is a direct replacement for the old hubs-wepabb Spring MVC webapp. As a number of our other front-end systems were already done in Grails, it made sense for us to migrate the hubs-webapp to Grails, as it meant there was a single layout file (and associated CSS files) required for all these apps. The webapp was written with most of the core functionality being in a Grails plugin, with a light weight client Grails app using the plugin and providing the skinning, as well as overriding any components that need customisation (i18n, views, custom URLs, etc). We aim to have the code up on Github soon (you can find it on the ALA Google code repo<https://code.google.com/p/ala-hubs/source/browse/#svn%2Ftrunk> until then - see biocache-hubs and generic-hub). Once up on Github, it will be easier for people to clone/fork our code and provide pull requests back to us, etc. We will make an announcement about the Github code repo, on this list, once we’ve moved the code over. If any of you have already created custom i18n translations for the old hubs-webapp code, could you please send me either a zip copy via email or the URL to your code repo and I’ll try and include the i18n codes into the GSP pages, etc. Cheers Nick -- Nick dos Remedios Atlas of Living Australia http://www.ala.org.au/

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Re: [Ala-portal] ALA harvest and indexing tool
by Tim Robertson [GBIF] 11 Jun '14

11 Jun '14

Hi Francisco, I am well thanks, and I hope you are too. The ALA tool can ingest DwC-A datasets from a URL (which could be an IPT or GBIF portal download for example) and they also support direct publication through file uploads. I am not sure if they have BioCASe, TAPIR and DiGIR support, but I *believe* not. It would not be particularly difficult with the GBIF crawler libraries however, for a Java developer to develop a crawler which produces DwC-A ready for ingestion into the ALA. Please can you ask these kind of questions to the user list (CC’ed) so you get the most accurate answers and so others who may have similar questions can search and discover them? Thanks, and I hope this helps, Tim On 11 Jun 2014, at 16:20, Francisco Moura <franciscomoura(a)gmail.com> wrote: > Hello Tim, how are you? > I hope you are doing well! > > Would you tell me wich tool ALA (Atlas of Living Australia) is using for harvest and indexing the occurrence datasets? > Are they using IPT to publish the occurrence datasets? > > Thank you again, > > Francisco Moura > +55 (31) 8277-8448 (Claro)

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