[Ala-portal] DwC-A loading problems
Daniel Lins
daniel.lins at gmail.com
Fri Jun 20 07:11:10 CEST 2014
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
Research Center on Biodiversity and Computing (Biocomp)
University of Sao Paulo, Brazil
daniellins at usp.br
daniel.lins at gmail.com
2014-06-18 6:15 GMT-03:00 <David.Martin at 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 at gmail.com]
> *Sent:* 18 June 2014 15:54
>
> *To:* Martin, Dave (CES, Black Mountain)
> *Cc:* ala-portal at 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
> Research Center on Biodiversity and Computing (Biocomp)
> University of Sao Paulo, Brazil
> daniellins at usp.br
> daniel.lins at gmail.com
>
>
>
> 2014-05-26 3:58 GMT-03:00 <David.Martin at 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-service/templates/config/biocache-config.properties
>>
>> Cheers
>>
>> Dave Martin
>> ALA
>>
>> ------------------------------
>> *From:* Daniel Lins [daniel.lins at gmail.com]
>> *Sent:* 26 May 2014 15:02
>> *To:* Martin, Dave (CES, Black Mountain)
>> *Cc:* ala-portal at 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
>> Research Center on Biodiversity and Computing (Biocomp)
>> University of Sao Paulo, Brazil
>> daniellins at usp.br
>> daniel.lins at gmail.com
>>
>>
>> 2014-05-09 2:14 GMT-03:00 <David.Martin at 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 at gmail.com]
>>> *Sent:* 09 May 2014 14:27
>>>
>>> *To:* Martin, Dave (CES, Black Mountain)
>>> *Cc:* ala-portal at 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 at 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 at gmail.com]
>>>>
>>>> *Sent:* 09 May 2014 13:59
>>>> *To:* Martin, Dave (CES, Black Mountain)
>>>> *Cc:* ala-portal at 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
>>>> Research Center on Biodiversity and Computing (Biocomp)
>>>> University of Sao Paulo, Brazil
>>>> daniellins at usp.br
>>>> daniel.lins at gmail.com
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2014-05-07 0:46 GMT-03:00 <David.Martin at 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 at gmail.com]
>>>>> *Sent:* 05 May 2014 15:39
>>>>> *To:* Quimby, Natasha (CES, Black Mountain)
>>>>> *Cc:* ala-portal at 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
>>>>> Research Center on Biodiversity and Computing (Biocomp)
>>>>> University of Sao Paulo, Brazil
>>>>> daniellins at usp.br
>>>>> daniel.lins at gmail.com
>>>>>
>>>>>
>>>>> 2014-04-28 3:52 GMT-03:00 Daniel Lins <daniel.lins at 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
>>>>>> Research Center on Biodiversity and Computing (Biocomp)
>>>>>> University of Sao Paulo, Brazil
>>>>>> daniellins at usp.br
>>>>>> daniel.lins at gmail.com
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2014-04-28 3:26 GMT-03:00 <Natasha.Quimby at 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:
>>>>>>> s*udo** 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:
>>>>>>> s*udo** 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 at gmail.com>
>>>>>>> Date: Monday, 28 April 2014 3:54 PM
>>>>>>> To: "ala-portal at lists.gbif.org" <ala-portal at lists.gbif.org
>>>>>>> <ala-portal at lists.gbif.org> <ala-portal at lists.gbif.org>
>>>>>>> <ala-portal at lists.gbif.org> <ala-portal at lists.gbif.org>
>>>>>>> <ala-portal at lists.gbif.org> <ala-portal at lists.gbif.org>>, "dos
>>>>>>> Remedios, Nick (CES, Black Mountain)" <Nick.Dosremedios at csiro.au>,
>>>>>>> "Martin, Dave (CES, Black Mountain)" <David.Martin at 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 at 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 at 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 at usp.br
>>>>>>> daniel.lins at gmail.com
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Daniel Lins da Silva
>>>>>> (Cel) 11 6144-4050
>>>>>> daniel.lins at gmail.com
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Daniel Lins da Silva
>>>>> (Cel) 11 6144-4050
>>>>> daniel.lins at gmail.com
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Daniel Lins da Silva
>>>> (Cel) 11 6144-4050
>>>> daniel.lins at gmail.com
>>>>
>>>
>>>
>>>
>>> --
>>> Daniel Lins da Silva
>>> (Cel) 11 6144-4050
>>> daniel.lins at gmail.com
>>>
>>
>>
>>
>> --
>> Daniel Lins da Silva
>> (Cel) 11 6144-4050
>> daniel.lins at gmail.com
>>
>
>
>
> --
> Daniel Lins da Silva
> (Cel) 11 6144-4050
> daniel.lins at gmail.com
>
--
Daniel Lins da Silva
(Cel) 11 6144-4050
daniel.lins at gmail.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.gbif.org/pipermail/ala-portal/attachments/20140620/1d7b0ef5/attachment-0001.html
-------------- next part --------------
biocache> load dr0
Darwin core archive loading
2014-06-20 01:48:06,589 INFO : [DataLoader] - Downloading zip file from http://192.168.15.132:8080/collectory/upload/1403239521145/dwca-ocorrencias_lobo_guara_1.zip
2014-06-20 01:48:06,612 INFO : [DataLoader] - Content-Disposition: attachment;filename=dwca-ocorrencias_lobo_guara_1.zip
2014-06-20 01:48:06,615 INFO : [DataLoader] -
Downloaded. File size:
2014-06-20 01:48:06,617 INFO : [DataLoader] - Extracting ZIP /data/biocache-load/dr0.zip
Extracting /data/biocache-load/dr0.zip to /data/biocache-load/dr0
Extracting to /data/biocache-load/dr0//meta.xml
Extracting to /data/biocache-load/dr0//eml.xml
Extracting to /data/biocache-load/dr0//occurrence.txt
2014-06-20 01:48:06,632 INFO : [DataLoader] - Archive extracted to directory: /data/biocache-load/dr0
2014-06-20 01:48:06,648 INFO : [DataLoader] - File last modified date: Fri Jun 20 01:48:06 BRT 2014
Loading archive /data/biocache-load/dr0 for resource dr0 with unique terms List(dwc:occurrenceID) stripping spaces false incremental false testing false
2014-06-20 01:48:07,398 INFO : [SolrIndexDAO] - Initialising the solr server http://192.168.15.132:8080/solr null null
2014-06-20 01:48:07,399 INFO : [SolrIndexDAO] - Initialising connection to SOLR server.....
2014-06-20 01:48:07,754 INFO : [SolrIndexDAO] - Initialising connection to SOLR server - done.
2014-06-20 01:48:07,932 INFO : [DataLoader] - The current institution codes for the data resource: Set()
2014-06-20 01:48:07,932 INFO : [DataLoader] - The current collection codes for the data resource: Set()
2014-06-20 01:48:09,883 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/15448/da7490ec-542a-4ce4-a3de-82d42c2302b0/lobo_guara.jpg
2014-06-20 01:48:19,684 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/23236/f790496d-8088-4dc4-8b21-c05beff463cf/M%C3%A4hnenwolf%20(Chrysocyon%20brachyurus)_315_B.jpg
2014-06-20 01:48:22,986 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/3941/d533d897-8d2a-436c-8d91-322a7765d99b/Chrysocyon%20brachyurus%20Maned%20wolf.jpg
2014-06-20 01:48:26,245 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/3241/cdc7c9ed-eb3a-4807-8bf2-508b2b61674f/0798.jpeg
2014-06-20 01:48:28,473 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/18584/efb97eab-0840-4900-b49e-892346a7c84c/4235657432_c40460509e.jpg
2014-06-20 01:48:30,847 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/10768/f05ce374-f616-4252-b3a4-6709e7c3e74a/Maned%20Wolf.jpg
2014-06-20 01:48:34,302 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/19839/2ba1760d-107e-4a4d-be32-81b72ca1b993/Loup_a_criniere_15.01.2011_-_225.JPG
2014-06-20 01:48:39,093 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/3101/16c3753e-138b-48a2-a606-45dd3394e399/animal_loboguara1_247_225_95.jpg
2014-06-20 01:48:40,343 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/13793/75f30058-375f-42e5-a566-25bb14664eb7/138908-004-DAC54ABC.jpg
2014-06-20 01:48:42,469 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/20590/2e00685d-c81e-4fce-b805-6bd710869128/chrysocyon_brachyurus_fd2355.jpg
2014-06-20 01:48:43,132 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/11519/60ee400e-69f8-4631-a6ca-77fdd9b58d5a/guara.jpg
2014-06-20 01:48:44,510 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/7507/ad4ee480-ca63-431a-b65c-31dffc75dc8d/tiring_weather_by_darksoul4life-d5nmy9p.jpg
2014-06-20 01:48:46,807 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/23039/15d28b1b-03e7-46ba-bed9-cfaebcc9a1f6/i-bb9a29728e13abc5d21a917c0b80d080-Chrysocyon.jpg
2014-06-20 01:48:48,921 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/13519/150ae131-bfdb-4df3-971c-448ad09f16aa/0167.jpeg
2014-06-20 01:48:50,228 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/13459/c636ffac-aed0-4a19-8341-759f4dda01d9/Caes-Selvagens-Brasileiros-Lobo-guara.jpg
2014-06-20 01:48:50,888 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/2554/c1b64cca-2c75-4735-acac-36d12a0d22a3/raposa.jpg
2014-06-20 01:48:51,949 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/21177/ddf3eaf6-55a4-4cdc-95a5-07113b7f46ea/tumblr_m06cie62q71qgzqeto1_500.jpg
2014-06-20 01:48:53,014 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/10521/26ed3ac7-5b15-412f-b6c5-f228b30f3d64/Chrysocyon.brachyurus.jpg
2014-06-20 01:48:55,741 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/3339/75fdf229-bfb9-46c9-9596-a22c70bda29c/lobo-guara.jpg
2014-06-20 01:48:58,274 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/27576/2a40070f-2b52-48c0-aac9-b94e93356356/Chrysocyon_brachyurus_-_Zoo_Frankfurt.jpg
2014-06-20 01:49:00,600 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/23229/1fcc357b-632f-4dc0-91df-b31cbdde3fc9/1022_500_380.png
2014-06-20 01:49:02,824 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/14068/4ae62e8c-34de-4af1-b57f-5c98f4a9fcb6/0799.jpeg
2014-06-20 01:49:04,438 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/17797/7c61234d-aeef-4104-aba8-d96c3821d29d/lobo-guarc3a1.jpg
2014-06-20 01:49:04,735 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/22461/f73a63a1-e361-449f-bcac-caa8e5ce5619/tumblr_m061iisXeO1qgzqeto1_500.jpg
2014-06-20 01:49:06,105 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/1895/1bc4166f-ff67-4a84-b19e-e784a310bd0d/wolf_jump.jpg
2014-06-20 01:49:07,266 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/7644/7bf3cb44-0734-4296-b8e4-14beeb01053a/jpg_Specie_arcaica_discende_da_un_antenato_dei_lupi_estinto_nel_Pleistocene_c_Giuseppe_Mazza.jpg
2014-06-20 01:49:08,017 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/9555/120185d0-86d8-4954-9aae-8c7b259af8a0/39f3123150b6018202404df8f2a11762.jpg
2014-06-20 01:49:09,789 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/17921/f28a9c71-3ba9-4a76-8597-f03a7ef3900b/037817_w_300.jpg
2014-06-20 01:49:12,281 INFO : [MediaStore] - File saved to: /data/biocache-media/dr0/26964/1b5b21fc-594a-46e6-b8db-cf37c50b8f7b/SuperStock_4168-2957.jpg
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
-------------------------------------------------------------------------------------------
biocache> process dr0
Processing dr0 incremental=false
2014-06-20 01:51:07,520 INFO : [Consumer] - Initialising thread: 0
2014-06-20 01:51:07,538 INFO : [Consumer] - Initialising thread: 1
2014-06-20 01:51:07,540 INFO : [Consumer] - Initialising thread: 2
2014-06-20 01:51:07,541 INFO : [Consumer] - Initialising thread: 3
2014-06-20 01:51:07,541 INFO : [ProcessWithActors] - Starting with dr0| endingwith dr0|~
2014-06-20 01:51:07,542 INFO : [ProcessWithActors] - Initialised actors...
2014-06-20 01:51:07,541 INFO : [Consumer] - In thread: 0
2014-06-20 01:51:07,550 INFO : [Consumer] - In thread: 1
2014-06-20 01:51:07,550 INFO : [Consumer] - In thread: 2
2014-06-20 01:51:07,557 INFO : [Consumer] - In thread: 3
2014-06-20 01:51:07,639 INFO : [ProcessWithActors] - First rowKey processed: dr0|null
2014-06-20 01:51:07,650 INFO : [ProcessWithActors] - Last row key processed: dr0|null
2014-06-20 01:51:07,660 INFO : [ProcessWithActors] - Finished.
2014-06-20 01:51:07,662 INFO : [Consumer] - Killing (Actor.act) thread: 1
2014-06-20 01:51:07,663 INFO : [Consumer] - Killing (Actor.act) thread: 2
2014-06-20 01:51:07,664 INFO : [Consumer] - Killing (Actor.act) thread: 3
2014-06-20 01:51:07,671 INFO : [AttributionDAO] - Calling web service for dr0
2014-06-20 01:51:07,787 INFO : [AttributionDAO] - Looking up collectory web service for ICMBIO|PARNASO
Jun 20, 2014 1:51:08 AM org.geotools.referencing.factory.epsg.ThreadedEpsgFactory <init>
INFO: Setting the EPSG factory org.geotools.referencing.factory.epsg.DefaultFactory to a 1800000ms timeout
Jun 20, 2014 1:51:08 AM org.geotools.referencing.factory.epsg.ThreadedEpsgFactory <init>
INFO: Setting the EPSG factory org.geotools.referencing.factory.epsg.ThreadedHsqlEpsgFactory to a 1800000ms timeout
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)
2014-06-20 01:51:21,713 WARN : [ALANameSearcher] - Unable to parse Australian bat lyssavirus. Name of type virus unparsable: Australian bat lyssavirus
2014-06-20 01:51:21,870 WARN : [ALANameSearcher] - Unable to parse Banana bract mosaic (Potyvirus). Name of type virus unparsable: Banana bract mosaic (Potyvirus)
2014-06-20 01:51:21,871 WARN : [ALANameSearcher] - Unable to parse Banana bunchy top (Babuvirus). Name of type virus unparsable: Banana bunchy top (Babuvirus)
2014-06-20 01:51:21,997 WARN : [ALANameSearcher] - Unable to parse Barley mild mosaic (Bymovirus). Name of type virus unparsable: Barley mild mosaic (Bymovirus)
2014-06-20 01:51:22,002 WARN : [ALANameSearcher] - Unable to parse Barley stripe mosaic (Hordeivirus). Name of type virus unparsable: Barley stripe mosaic (Hordeivirus)
2014-06-20 01:51:22,003 WARN : [ALANameSearcher] - Unable to parse Barley yellow mosaic (Bymovirus). Name of type virus unparsable: Barley yellow mosaic (Bymovirus)
2014-06-20 01:51:22,003 WARN : [ALANameSearcher] - Unable to parse Barley yellow striate mosaic (Cytorhabdovirus). Name of type virus unparsable: Barley yellow striate mosaic (Cytorhabdovirus)
2014-06-20 01:51:22,008 WARN : [ALANameSearcher] - Unable to parse Barley yellow striate mosaic (Cytorhabdovirus). Name of type virus unparsable: Barley yellow striate mosaic (Cytorhabdovirus)
2014-06-20 01:51:22,018 WARN : [ALANameSearcher] - Unable to parse Bean yellow mosaic (Potyvirus). Name of type virus unparsable: Bean yellow mosaic (Potyvirus)
2014-06-20 01:51:22,019 WARN : [ALANameSearcher] - Unable to parse Bean yellow veinbanding (Umbravirus). Name of type virus unparsable: Bean yellow veinbanding (Umbravirus)
2014-06-20 01:51:22,021 WARN : [ALANameSearcher] - Unable to parse Begomovirus cotton leaf curl. Name of type virus unparsable: Begomovirus cotton leaf curl
2014-06-20 01:51:22,038 WARN : [ALANameSearcher] - Unable to parse Bison bison X Bos taurus (more than 37.5%). Name of type hybrid unparsable: Bison bison X Bos taurus (more than 37.5%)
2014-06-20 01:51:22,039 WARN : [ALANameSearcher] - Unable to parse Black queen cell (Cripavirus). Name of type virus unparsable: Black queen cell (Cripavirus)
2014-06-20 01:51:22,044 WARN : [ALANameSearcher] - Unable to parse Blueberry leaf mottle (Nepovirus). Name of type virus unparsable: Blueberry leaf mottle (Nepovirus)
2014-06-20 01:51:22,110 WARN : [ALANameSearcher] - Unable to parse Broad bean mottle (Bromovirus). Name of type virus unparsable: Broad bean mottle (Bromovirus)
2014-06-20 01:51:22,111 WARN : [ALANameSearcher] - Unable to parse Broad bean necrosis (Furovirus). Name of type virus unparsable: Broad bean necrosis (Furovirus)
2014-06-20 01:51:22,111 WARN : [ALANameSearcher] - Unable to parse Broad bean severe chlorosis (Unclassified). Name of type blacklisted unparsable: Broad bean severe chlorosis (Unclassified)
2014-06-20 01:51:22,112 WARN : [ALANameSearcher] - Unable to parse Broad bean stain (Comovirus). Name of type virus unparsable: Broad bean stain (Comovirus)
2014-06-20 01:51:22,112 WARN : [ALANameSearcher] - Unable to parse Broad bean true mosaic (Comovirus). Name of type virus unparsable: Broad bean true mosaic (Comovirus)
2014-06-20 01:51:22,113 WARN : [ALANameSearcher] - Unable to parse Broad bean yellow vein (Cytorhabdovirus). Name of type virus unparsable: Broad bean yellow vein (Cytorhabdovirus)
2014-06-20 01:51:22,151 WARN : [ALANameSearcher] - Unable to parse CLCuD complex (Begomoviruses). Name of type virus unparsable: CLCuD complex (Begomoviruses)
2014-06-20 01:51:22,396 WARN : [ALANameSearcher] - Unable to parse Canis lupus dingo x Canis lupus familiaris. Name of type hybrid unparsable: Canis lupus dingo x Canis lupus familiaris
2014-06-20 01:51:22,428 WARN : [ALANameSearcher] - Unable to parse Carrot mosaic (Potyvirus). Name of type virus unparsable: Carrot mosaic (Potyvirus)
2014-06-20 01:51:22,431 WARN : [ALANameSearcher] - Unable to parse Carrot thin leaf (Potyvirus). Name of type virus unparsable: Carrot thin leaf (Potyvirus)
2014-06-20 01:51:22,555 WARN : [ALANameSearcher] - Unable to parse Cherry A (Capillovirus). Name of type virus unparsable: Cherry A (Capillovirus)
2014-06-20 01:51:22,556 WARN : [ALANameSearcher] - Unable to parse Cherry leaf roll (Nepovirus). Name of type virus unparsable: Cherry leaf roll (Nepovirus)
2014-06-20 01:51:22,556 WARN : [ALANameSearcher] - Unable to parse Cherry leaf roll (Nepovirus) (exotic strains). Name of type virus unparsable: Cherry leaf roll (Nepovirus) (exotic strains)
2014-06-20 01:51:22,557 WARN : [ALANameSearcher] - Unable to parse Cherry leafroll (Nepovirus). Name of type virus unparsable: Cherry leafroll (Nepovirus)
2014-06-20 01:51:22,557 WARN : [ALANameSearcher] - Unable to parse Cherry mottle leaf (Trichovirus). Name of type virus unparsable: Cherry mottle leaf (Trichovirus)
2014-06-20 01:51:22,559 WARN : [ALANameSearcher] - Unable to parse Cherry A (CVA, Capillovirus). Name of type virus unparsable: Cherry A (CVA, Capillovirus)
2014-06-20 01:51:22,559 WARN : [ALANameSearcher] - Unable to parse Chickpea bushy dwarf (Potyvirus). Name of type virus unparsable: Chickpea bushy dwarf (Potyvirus)
2014-06-20 01:51:22,561 WARN : [ALANameSearcher] - Unable to parse Chickpea chlorotic dwarf (Geminivirus). Name of type virus unparsable: Chickpea chlorotic dwarf (Geminivirus)
2014-06-20 01:51:22,561 WARN : [ALANameSearcher] - Unable to parse Chickpea chlorotic stunt (Polerovirus). Name of type virus unparsable: Chickpea chlorotic stunt (Polerovirus)
2014-06-20 01:51:22,562 WARN : [ALANameSearcher] - Unable to parse Chickpea distortion mosaic (Potyvirus). Name of type virus unparsable: Chickpea distortion mosaic (Potyvirus)
2014-06-20 01:51:22,562 WARN : [ALANameSearcher] - Unable to parse Chickpea filiform (Potyvirus). Name of type virus unparsable: Chickpea filiform (Potyvirus)
2014-06-20 01:51:22,611 WARN : [ALANameSearcher] - Unable to parse Chrysanthemum stem necrosis (Tospovirus). Name of type virus unparsable: Chrysanthemum stem necrosis (Tospovirus)
2014-06-20 01:51:22,622 WARN : [ALANameSearcher] - Unable to parse Citrus leprosies rhabdovirus. Name of type virus unparsable: Citrus leprosies rhabdovirus
2014-06-20 01:51:22,623 WARN : [ALANameSearcher] - Unable to parse Citrus tristeza (Closterovirus) (mandarin stem-pitting strain). Name of type virus unparsable: Citrus tristeza (Closterovirus) (mandarin stem-pitting strain)
2014-06-20 01:51:22,623 WARN : [ALANameSearcher] - Unable to parse Citrus tristeza (Closterovirus) (sweet orange stem-pitting strain). Name of type virus unparsable: Citrus tristeza (Closterovirus) (sweet orange stem-pitting strain)
2014-06-20 01:51:22,623 WARN : [ALANameSearcher] - Unable to parse Citrus yellow mosaic (Badnavirus). Name of type virus unparsable: Citrus yellow mosaic (Badnavirus)
2014-06-20 01:51:22,637 WARN : [ALANameSearcher] - Unable to parse Closteroviruses. Name of type virus unparsable: Closteroviruses
2014-06-20 01:51:22,637 WARN : [ALANameSearcher] - Unable to parse Clover yellow mosaic (Potexvirus). Name of type virus unparsable: Clover yellow mosaic (Potexvirus)
2014-06-20 01:51:22,657 WARN : [ALANameSearcher] - Unable to parse Comoviridae: Nepovirus. Name of type virus unparsable: Comoviridae: Nepovirus
2014-06-20 01:51:22,658 WARN : [ALANameSearcher] - Unable to parse Complex infection of Groundnut rosette (Umbravirus), Groundnut assister (Luteovirus), Chlorotic rosette, green rosette & mosaic rosette. Name of type virus unparsable: Complex infection of Groundnut rosette (Umbravirus), Groundnut assister (Luteovirus), Chlorotic rosette, green rosette & mosaic rosette
2014-06-20 01:51:22,713 WARN : [ALANameSearcher] - Unable to parse Cotton leaf curl (Begomovirus). Name of type virus unparsable: Cotton leaf curl (Begomovirus)
2014-06-20 01:51:22,714 WARN : [ALANameSearcher] - Unable to parse Cowpea mild mottle (Carlavirus). Name of type virus unparsable: Cowpea mild mottle (Carlavirus)
2014-06-20 01:51:22,725 WARN : [ALANameSearcher] - Unable to parse Criniviruses. Name of type virus unparsable: Criniviruses
2014-06-20 01:51:22,822 WARN : [ALANameSearcher] - Unable to parse Cucurbit aphid-borne yellow (Polerovirus). Name of type virus unparsable: Cucurbit aphid-borne yellow (Polerovirus)
2014-06-20 01:51:22,832 WARN : [ALANameSearcher] - Unable to parse Cucurbit yellow stunting disorder (Crinivirus). Name of type virus unparsable: Cucurbit yellow stunting disorder (Crinivirus)
2014-06-20 01:51:22,877 WARN : [ALANameSearcher] - Unable to parse Cycas media subsp. banksii x C.platyphylla. Name of type hybrid unparsable: Cycas media subsp. banksii x C.platyphylla
2014-06-20 01:51:22,910 WARN : [ALANameSearcher] - Unable to parse Cynodon chlorotic streak (Nucleorhabdovirus) (CCSV). Name of type virus unparsable: Cynodon chlorotic streak (Nucleorhabdovirus) (CCSV)
2014-06-20 01:51:23,274 WARN : [ALANameSearcher] - Unable to parse Deformed wing (Iflavirus). Name of type virus unparsable: Deformed wing (Iflavirus)
2014-06-20 01:51:23,293 WARN : [ALANameSearcher] - Unable to parse Dendrobium kingianum x D.speciosum. Name of type hybrid unparsable: Dendrobium kingianum x D.speciosum
2014-06-20 01:51:23,301 WARN : [ALANameSearcher] - Unable to parse Dendrobium speciosum subsp. grandiflorum x D.speciosum subsp. hillii. Name of type hybrid unparsable: Dendrobium speciosum subsp. grandiflorum x D.speciosum subsp. hillii
2014-06-20 01:51:23,378 WARN : [ALANameSearcher] - Unable to parse Diuris alba x D.chrysantha. Name of type hybrid unparsable: Diuris alba x D.chrysantha
2014-06-20 01:51:23,547 WARN : [ALANameSearcher] - Unable to parse Eucalyptus absita x loxophleba. Name of type hybrid unparsable: Eucalyptus absita x loxophleba
2014-06-20 01:51:23,552 WARN : [ALANameSearcher] - Unable to parse Eucalyptus buprestium x erectifolia. Name of type hybrid unparsable: Eucalyptus buprestium x erectifolia
2014-06-20 01:51:23,553 WARN : [ALANameSearcher] - Unable to parse Eucalyptus buprestium x ligulata. Name of type hybrid unparsable: Eucalyptus buprestium x ligulata
2014-06-20 01:51:23,553 WARN : [ALANameSearcher] - Unable to parse Eucalyptus buprestium x marginata. Name of type hybrid unparsable: Eucalyptus buprestium x marginata
2014-06-20 01:51:23,553 WARN : [ALANameSearcher] - Unable to parse Eucalyptus buprestium x staeri. Name of type hybrid unparsable: Eucalyptus buprestium x staeri
2014-06-20 01:51:23,560 WARN : [ALANameSearcher] - Unable to parse Eucalyptus dielsii x platypus. Name of type hybrid unparsable: Eucalyptus dielsii x platypus
2014-06-20 01:51:23,572 WARN : [ALANameSearcher] - Unable to parse Eucalyptus loxophleba x wandoo. Name of type hybrid unparsable: Eucalyptus loxophleba x wandoo
2014-06-20 01:51:23,573 WARN : [ALANameSearcher] - Unable to parse Eucalyptus macrocarpa x pyriformis. Name of type hybrid unparsable: Eucalyptus macrocarpa x pyriformis
2014-06-20 01:51:23,574 WARN : [ALANameSearcher] - Unable to parse Eucalyptus marginata x megacarpa. Name of type hybrid unparsable: Eucalyptus marginata x megacarpa
2014-06-20 01:51:23,574 WARN : [ALANameSearcher] - Unable to parse Eucalyptus marginata x pachyloma. Name of type hybrid unparsable: Eucalyptus marginata x pachyloma
2014-06-20 01:51:23,583 WARN : [ALANameSearcher] - Unable to parse Eucalyptus preissiana x staeri. Name of type hybrid unparsable: Eucalyptus preissiana x staeri
2014-06-20 01:51:23,586 WARN : [ALANameSearcher] - Unable to parse Eucalyptus rhodantha var. x petiolaris. Name of type hybrid unparsable: Eucalyptus rhodantha var. x petiolaris
2014-06-20 01:51:23,630 WARN : [ALANameSearcher] - Unable to parse Faba bean necrotic yellows (Nanovirus). Name of type virus unparsable: Faba bean necrotic yellows (Nanovirus)
2014-06-20 01:51:23,635 WARN : [ALANameSearcher] - Unable to parse Fiji Disease Virus (Fijivirus). Name of type virus unparsable: Fiji Disease Virus (Fijivirus)
2014-06-20 01:51:23,647 WARN : [ALANameSearcher] - Unable to parse Flexiviridae: Potato Virus S. Name of type virus unparsable: Flexiviridae: Potato Virus S
2014-06-20 01:51:23,649 WARN : [ALANameSearcher] - Unable to parse Foxtail mosaic (Potexvirus). Name of type virus unparsable: Foxtail mosaic (Potexvirus)
2014-06-20 01:51:23,713 WARN : [ALANameSearcher] - Unable to parse Geminiviruses. Name of type virus unparsable: Geminiviruses
2014-06-20 01:51:23,729 WARN : [ALANameSearcher] - Unable to parse Ginger chlorotic fleck Sobemovirus. Name of type virus unparsable: Ginger chlorotic fleck Sobemovirus
2014-06-20 01:51:23,772 WARN : [ALANameSearcher] - Unable to parse Grapevine B vitivirus. Name of type virus unparsable: Grapevine B vitivirus
2014-06-20 01:51:23,773 WARN : [ALANameSearcher] - Unable to parse Grapevine Bulgarian latent (Nepovirus). Name of type virus unparsable: Grapevine Bulgarian latent (Nepovirus)
2014-06-20 01:51:23,773 WARN : [ALANameSearcher] - Unable to parse Grapevine Joannes Seyve (Nepovirus). Name of type virus unparsable: Grapevine Joannes Seyve (Nepovirus)
2014-06-20 01:51:23,774 WARN : [ALANameSearcher] - Unable to parse Grapevine Tunisian ringspot (Nepovirus). Name of type virus unparsable: Grapevine Tunisian ringspot (Nepovirus)
2014-06-20 01:51:23,774 WARN : [ALANameSearcher] - Unable to parse Grapevine ajinashika (Luteovirus). Name of type virus unparsable: Grapevine ajinashika (Luteovirus)
2014-06-20 01:51:23,775 WARN : [ALANameSearcher] - Unable to parse Grapevine asteroid mosaic associated (Marafivirus). Name of type virus unparsable: Grapevine asteroid mosaic associated (Marafivirus)
2014-06-20 01:51:23,775 WARN : [ALANameSearcher] - Unable to parse Grapevine chrome mosaic (Nepovirus). Name of type virus unparsable: Grapevine chrome mosaic (Nepovirus)
2014-06-20 01:51:23,776 WARN : [ALANameSearcher] - Unable to parse Grapevine inner necrosis (Trichovirus). Name of type virus unparsable: Grapevine inner necrosis (Trichovirus)
2014-06-20 01:51:23,777 WARN : [ALANameSearcher] - Unable to parse Grapevine D (Vitivirus). Name of type virus unparsable: Grapevine D (Vitivirus)
2014-06-20 01:51:23,777 WARN : [ALANameSearcher] - Unable to parse Grapevine yellow dwarf (Luteovirus). Name of type virus unparsable: Grapevine yellow dwarf (Luteovirus)
2014-06-20 01:51:23,778 WARN : [ALANameSearcher] - Unable to parse Grapevine yellow vein mosaic (Nepovirus). Name of type virus unparsable: Grapevine yellow vein mosaic (Nepovirus)
2014-06-20 01:51:23,833 WARN : [ALANameSearcher] - Unable to parse Guinea grass mosaic (Potyvirus) (GGMV). Name of type virus unparsable: Guinea grass mosaic (Potyvirus) (GGMV)
2014-06-20 01:51:23,895 WARN : [ALANameSearcher] - Unable to parse Hellebore Net Necrosis Virus. Name of type virus unparsable: Hellebore Net Necrosis Virus
2014-06-20 01:51:23,962 WARN : [ALANameSearcher] - Unable to parse High plains tenuivirus. Name of type virus unparsable: High plains tenuivirus
2014-06-20 01:51:23,963 WARN : [ALANameSearcher] - Unable to parse High plains (Unassigned). Name of type blacklisted unparsable: High plains (Unassigned)
2014-06-20 01:51:24,029 WARN : [ALANameSearcher] - Unable to parse Impatiens necrotic spot (Tospovirus). Name of type virus unparsable: Impatiens necrotic spot (Tospovirus)
2014-06-20 01:51:24,147 WARN : [ALANameSearcher] - Unable to parse Lettuce infectious yellows (Closterovirus). Name of type virus unparsable: Lettuce infectious yellows (Closterovirus)
2014-06-20 01:51:24,148 WARN : [ALANameSearcher] - Unable to parse Lettuce infectious yellows (Crinivirus). Name of type virus unparsable: Lettuce infectious yellows (Crinivirus)
2014-06-20 01:51:24,218 WARN : [ALANameSearcher] - Unable to parse Little cherry and (Unassigned). Name of type blacklisted unparsable: Little cherry and (Unassigned)
2014-06-20 01:51:24,219 WARN : [ALANameSearcher] - Unable to parse Little cherry and (Unassigned Closteroviridae). Name of type blacklisted unparsable: Little cherry and (Unassigned Closteroviridae)
2014-06-20 01:51:24,230 WARN : [ALANameSearcher] - Unable to parse Luteovirus (suspected). Name of type virus unparsable: Luteovirus (suspected)
2014-06-20 01:51:24,264 WARN : [ALANameSearcher] - Unable to parse Macrozamia fearnsidei x M.moorei. Name of type hybrid unparsable: Macrozamia fearnsidei x M.moorei
2014-06-20 01:51:24,268 WARN : [ALANameSearcher] - Unable to parse Macrozamia lomandroides x M.pauli-guilielmi. Name of type hybrid unparsable: Macrozamia lomandroides x M.pauli-guilielmi
2014-06-20 01:51:24,269 WARN : [ALANameSearcher] - Unable to parse Macrozamia lucida x M.macleayi. Name of type hybrid unparsable: Macrozamia lucida x M.macleayi
2014-06-20 01:51:24,284 WARN : [ALANameSearcher] - Unable to parse Maize chlorotic dwarf (Waikavirus) (MCDV). Name of type virus unparsable: Maize chlorotic dwarf (Waikavirus) (MCDV)
2014-06-20 01:51:24,285 WARN : [ALANameSearcher] - Unable to parse Maize chlorotic mottle (Machlomovirus). Name of type virus unparsable: Maize chlorotic mottle (Machlomovirus)
2014-06-20 01:51:24,285 WARN : [ALANameSearcher] - Unable to parse Maize dwarf mosaic (Potyvirus). Name of type virus unparsable: Maize dwarf mosaic (Potyvirus)
2014-06-20 01:51:24,286 WARN : [ALANameSearcher] - Unable to parse Maize eyespot (Unclassified). Name of type blacklisted unparsable: Maize eyespot (Unclassified)
2014-06-20 01:51:24,287 WARN : [ALANameSearcher] - Unable to parse Maize gooseneck stripe (Unclassified). Name of type blacklisted unparsable: Maize gooseneck stripe (Unclassified)
2014-06-20 01:51:24,287 WARN : [ALANameSearcher] - Unable to parse Maize iranian mosaic (Nucleo-rhabdovirus). Name of type virus unparsable: Maize iranian mosaic (Nucleo-rhabdovirus)
2014-06-20 01:51:24,288 WARN : [ALANameSearcher] - Unable to parse Maize line (unclassified). Name of type blacklisted unparsable: Maize line (unclassified)
2014-06-20 01:51:24,288 WARN : [ALANameSearcher] - Unable to parse Maize mosaic (Nucleo-rhabdovirus). Name of type virus unparsable: Maize mosaic (Nucleo-rhabdovirus)
2014-06-20 01:51:24,291 WARN : [ALANameSearcher] - Unable to parse Maize mottle (Begomovirus) syn. Chlorotic stunt. Name of type virus unparsable: Maize mottle (Begomovirus) syn. Chlorotic stunt
2014-06-20 01:51:24,291 WARN : [ALANameSearcher] - Unable to parse Maize raya gruesa (unclassified). Name of type blacklisted unparsable: Maize raya gruesa (unclassified)
2014-06-20 01:51:24,292 WARN : [ALANameSearcher] - Unable to parse Maize rayado fino (Marafivirus). Name of type virus unparsable: Maize rayado fino (Marafivirus)
2014-06-20 01:51:24,293 WARN : [ALANameSearcher] - Unable to parse Maize rough dwarf (Fijivirus). Name of type virus unparsable: Maize rough dwarf (Fijivirus)
2014-06-20 01:51:24,293 WARN : [ALANameSearcher] - Unable to parse Maize streak (Mastrevirus). Name of type virus unparsable: Maize streak (Mastrevirus)
2014-06-20 01:51:24,294 WARN : [ALANameSearcher] - Unable to parse Maize streak (Monogeminivirus) (MSV). Name of type virus unparsable: Maize streak (Monogeminivirus) (MSV)
2014-06-20 01:51:24,294 WARN : [ALANameSearcher] - Unable to parse Maize white line mosaic (Unclassified). Name of type blacklisted unparsable: Maize white line mosaic (Unclassified)
2014-06-20 01:51:24,405 WARN : [ALANameSearcher] - Unable to parse Melon yellow spot (Tospovirus). Name of type virus unparsable: Melon yellow spot (Tospovirus)
2014-06-20 01:51:24,496 WARN : [ALANameSearcher] - Unable to parse Milk vetch dwarf nanovirus. Name of type virus unparsable: Milk vetch dwarf nanovirus
2014-06-20 01:51:24,497 WARN : [ALANameSearcher] - Unable to parse Milk vetch dwarf (Nanovirus). Name of type virus unparsable: Milk vetch dwarf (Nanovirus)
2014-06-20 01:51:24,621 WARN : [ALANameSearcher] - Unable to parse Myrobalan latent ringspot (Nepovirus). Name of type virus unparsable: Myrobalan latent ringspot (Nepovirus)
2014-06-20 01:51:24,665 WARN : [ALANameSearcher] - Unable to parse Nepovirus cherry leaf roll. Name of type virus unparsable: Nepovirus cherry leaf roll
2014-06-20 01:51:24,670 WARN : [ALANameSearcher] - Unable to parse Nepoviruses. Name of type virus unparsable: Nepoviruses
2014-06-20 01:51:24,670 WARN : [ALANameSearcher] - Unable to parse Nepoviruses other than ArMV. Name of type virus unparsable: Nepoviruses other than ArMV
2014-06-20 01:51:24,738 WARN : [ALANameSearcher] - Unable to parse Oat blue dwarf (Marafivirus). Name of type virus unparsable: Oat blue dwarf (Marafivirus)
2014-06-20 01:51:24,744 WARN : [ALANameSearcher] - Unable to parse Oat chlorotic stunt (Avenavirus). Name of type virus unparsable: Oat chlorotic stunt (Avenavirus)
2014-06-20 01:51:24,744 WARN : [ALANameSearcher] - Unable to parse Oat golden stripe (Furovirus). Name of type virus unparsable: Oat golden stripe (Furovirus)
2014-06-20 01:51:24,745 WARN : [ALANameSearcher] - Unable to parse Oat mosaic (Potyvirus). Name of type virus unparsable: Oat mosaic (Potyvirus)
2014-06-20 01:51:24,745 WARN : [ALANameSearcher] - Unable to parse Oat sterile dwarf (Fujivirus). Name of type virus unparsable: Oat sterile dwarf (Fujivirus)
2014-06-20 01:51:24,776 WARN : [ALANameSearcher] - Unable to parse Olive latent ringspot (Nepovirus). Name of type virus unparsable: Olive latent ringspot (Nepovirus)
2014-06-20 01:51:24,785 WARN : [ALANameSearcher] - Unable to parse Olive leaf yellowing associated (Closterovirus). Name of type virus unparsable: Olive leaf yellowing associated (Closterovirus)
2014-06-20 01:51:24,785 WARN : [ALANameSearcher] - Unable to parse Olive semi latent (Undetermined). Name of type blacklisted unparsable: Olive semi latent (Undetermined)
2014-06-20 01:51:24,786 WARN : [ALANameSearcher] - Unable to parse Olive vein yellowing-associated (Potexvirus). Name of type virus unparsable: Olive vein yellowing-associated (Potexvirus)
2014-06-20 01:51:24,787 WARN : [ALANameSearcher] - Unable to parse Onion mite-borne latent potexvirus. Name of type virus unparsable: Onion mite-borne latent potexvirus
2014-06-20 01:51:24,846 WARN : [ALANameSearcher] - Unable to parse Papaya apical necrosis rhabdovirus. Name of type virus unparsable: Papaya apical necrosis rhabdovirus
2014-06-20 01:51:24,849 WARN : [ALANameSearcher] - Unable to parse Papaya leaf curl (several Begomoviruses can cause this disease). Name of type virus unparsable: Papaya leaf curl (several Begomoviruses can cause this disease)
2014-06-20 01:51:24,850 WARN : [ALANameSearcher] - Unable to parse Papaya leaf medium distortion mosaic (Potyvirus). Name of type virus unparsable: Papaya leaf medium distortion mosaic (Potyvirus)
2014-06-20 01:51:24,851 WARN : [ALANameSearcher] - Unable to parse Papaya mosaic (Potexvirus). Name of type virus unparsable: Papaya mosaic (Potexvirus)
2014-06-20 01:51:24,851 WARN : [ALANameSearcher] - Unable to parse Papaya ringspot Type P (Potyvirus). Name of type virus unparsable: Papaya ringspot Type P (Potyvirus)
2014-06-20 01:51:24,866 WARN : [ALANameSearcher] - Unable to parse Passionfruit Sri Lankan mottle potyvirus. Name of type virus unparsable: Passionfruit Sri Lankan mottle potyvirus
2014-06-20 01:51:24,868 WARN : [ALANameSearcher] - Unable to parse Passionfruit vein clearing rhabdovirus. Name of type virus unparsable: Passionfruit vein clearing rhabdovirus
2014-06-20 01:51:24,869 WARN : [ALANameSearcher] - Unable to parse Pea early browning (Tobravirus). Name of type virus unparsable: Pea early browning (Tobravirus)
2014-06-20 01:51:24,870 WARN : [ALANameSearcher] - Unable to parse Pea enation mosaic (Enamovirus + Umbravirus). Name of type virus unparsable: Pea enation mosaic (Enamovirus + Umbravirus)
2014-06-20 01:51:24,870 WARN : [ALANameSearcher] - Unable to parse Pea mild mosaic (Comovirus). Name of type virus unparsable: Pea mild mosaic (Comovirus)
2014-06-20 01:51:24,871 WARN : [ALANameSearcher] - Unable to parse Pea stem necrosis (Unclassified). Name of type blacklisted unparsable: Pea stem necrosis (Unclassified)
2014-06-20 01:51:24,871 WARN : [ALANameSearcher] - Unable to parse Pea streak (Carlavirus). Name of type virus unparsable: Pea streak (Carlavirus)
2014-06-20 01:51:24,871 WARN : [ALANameSearcher] - Unable to parse Pea stunt (Cucumovirus). Name of type virus unparsable: Pea stunt (Cucumovirus)
2014-06-20 01:51:24,873 WARN : [ALANameSearcher] - Unable to parse Peach enation (Nepovirus). Name of type virus unparsable: Peach enation (Nepovirus)
2014-06-20 01:51:24,875 WARN : [ALANameSearcher] - Unable to parse Peach rosette mosaic (Nepovirus). Name of type virus unparsable: Peach rosette mosaic (Nepovirus)
2014-06-20 01:51:24,875 WARN : [ALANameSearcher] - Unable to parse Peach rosette mosaic (Nepovirus). Name of type virus unparsable: Peach rosette mosaic (Nepovirus)
2014-06-20 01:51:24,876 WARN : [ALANameSearcher] - Unable to parse Peanut Clump Virus. Name of type virus unparsable: Peanut Clump Virus
2014-06-20 01:51:24,877 WARN : [ALANameSearcher] - Unable to parse Peanut clump (Pecluvirus). Name of type virus unparsable: Peanut clump (Pecluvirus)
2014-06-20 01:51:24,877 WARN : [ALANameSearcher] - Unable to parse Peanut stripe (Potyvirus). Name of type virus unparsable: Peanut stripe (Potyvirus)
2014-06-20 01:51:24,878 WARN : [ALANameSearcher] - Unable to parse Peanut stunt (Cucumovirus). Name of type virus unparsable: Peanut stunt (Cucumovirus)
2014-06-20 01:51:24,879 WARN : [ALANameSearcher] - Unable to parse Pelargonium flower break (Carmovirus). Name of type virus unparsable: Pelargonium flower break (Carmovirus)
2014-06-20 01:51:24,884 WARN : [ALANameSearcher] - Unable to parse Pepino mosaic potexvirus. Name of type virus unparsable: Pepino mosaic potexvirus
2014-06-20 01:51:24,885 WARN : [ALANameSearcher] - Unable to parse Pepino mosaic (Potexvirus). Name of type virus unparsable: Pepino mosaic (Potexvirus)
2014-06-20 01:51:24,906 WARN : [ALANameSearcher] - Unable to parse Petunia asteroid mosaic (Tombusvirus). Name of type virus unparsable: Petunia asteroid mosaic (Tombusvirus)
2014-06-20 01:51:24,998 WARN : [ALANameSearcher] - Unable to parse Plantago mottle (Tymovirus). Name of type virus unparsable: Plantago mottle (Tymovirus)
2014-06-20 01:51:25,018 WARN : [ALANameSearcher] - Unable to parse Plum pox potyvirus. Name of type virus unparsable: Plum pox potyvirus
2014-06-20 01:51:25,019 WARN : [ALANameSearcher] - Unable to parse Plum pox (Potyvirus). Name of type virus unparsable: Plum pox (Potyvirus)
2014-06-20 01:51:25,036 WARN : [ALANameSearcher] - Unable to parse Potyviridae: Potato A potyvirus. Potato A potyvirus. Name of type virus unparsable: Potyviridae: Potato A potyvirus. Potato A potyvirus
2014-06-20 01:51:25,037 WARN : [ALANameSearcher] - Unable to parse Potyviridae: Potato Virus V. Name of type virus unparsable: Potyviridae: Potato Virus V
2014-06-20 01:51:25,037 WARN : [ALANameSearcher] - Unable to parse Potyviridae: Potato Virus Y. There are general strain groups – PVYO, PVYN, PVYC (and some others that do not fit into these groups).. Name of type virus unparsable: Potyviridae: Potato Virus Y. There are general strain groups – PVYO, PVYN, PVYC (and some others that do not fit into these groups).
2014-06-20 01:51:25,061 WARN : [ALANameSearcher] - Unable to parse Prosopis glandulosa Torr. x Prosopis velutina Wooton. Name of type hybrid unparsable: Prosopis glandulosa Torr. x Prosopis velutina Wooton
2014-06-20 01:51:25,153 WARN : [ALANameSearcher] - Unable to parse Raboviruses. Name of type virus unparsable: Raboviruses
2014-06-20 01:51:25,154 WARN : [ALANameSearcher] - Unable to parse Radish mosaic (Comovirus). Name of type virus unparsable: Radish mosaic (Comovirus)
2014-06-20 01:51:25,161 WARN : [ALANameSearcher] - Unable to parse Raspberry ringspot (Nepovirus). Name of type virus unparsable: Raspberry ringspot (Nepovirus)
2014-06-20 01:51:25,161 WARN : [ALANameSearcher] - Unable to parse Raspberry ringspot (Nepovirus). Name of type virus unparsable: Raspberry ringspot (Nepovirus)
2014-06-20 01:51:25,162 WARN : [ALANameSearcher] - Unable to parse Raspberry ringspot (Nepovirus). Name of type virus unparsable: Raspberry ringspot (Nepovirus)
2014-06-20 01:51:25,165 WARN : [ALANameSearcher] - Unable to parse Red clover vein mosaic (Carlavirus). Name of type virus unparsable: Red clover vein mosaic (Carlavirus)
2014-06-20 01:51:25,167 WARN : [ALANameSearcher] - Unable to parse Reovirus. Name of type virus unparsable: Reovirus
2014-06-20 01:51:25,187 WARN : [ALANameSearcher] - Unable to parse Rice black streaked dwarf (Fijivirus). Name of type virus unparsable: Rice black streaked dwarf (Fijivirus)
2014-06-20 01:51:25,187 WARN : [ALANameSearcher] - Unable to parse Rice hoja blanca (Tenuivirus). Name of type virus unparsable: Rice hoja blanca (Tenuivirus)
2014-06-20 01:51:25,188 WARN : [ALANameSearcher] - Unable to parse Rice stripe tenuivirus. Name of type virus unparsable: Rice stripe tenuivirus
2014-06-20 01:51:25,188 WARN : [ALANameSearcher] - Unable to parse Rice stripe (Tenuivirus). Name of type virus unparsable: Rice stripe (Tenuivirus)
2014-06-20 01:51:25,195 WARN : [ALANameSearcher] - Unable to parse Roditis leaf discoloration (Carmovirus). Name of type virus unparsable: Roditis leaf discoloration (Carmovirus)
2014-06-20 01:51:25,212 WARN : [ALANameSearcher] - Unable to parse Satsuma dwarf (Nepovirus). Name of type virus unparsable: Satsuma dwarf (Nepovirus)
2014-06-20 01:51:25,300 WARN : [ALANameSearcher] - Unable to parse Shallot latent carlavirus. Name of type virus unparsable: Shallot latent carlavirus
2014-06-20 01:51:25,300 WARN : [ALANameSearcher] - Unable to parse Shallot mite-borne latent potexvirus. Name of type virus unparsable: Shallot mite-borne latent potexvirus
2014-06-20 01:51:25,301 WARN : [ALANameSearcher] - Unable to parse Shallot yellow stripe potyvirus. Name of type virus unparsable: Shallot yellow stripe potyvirus
2014-06-20 01:51:25,304 WARN : [ALANameSearcher] - Unable to parse Sint-Jan’s onion latent carlavirus. Name of type virus unparsable: Sint-Jan’s onion latent carlavirus
2014-06-20 01:51:25,307 WARN : [ALANameSearcher] - Unable to parse Slow paralysis (Iflavirus). Name of type virus unparsable: Slow paralysis (Iflavirus)
2014-06-20 01:51:25,310 WARN : [ALANameSearcher] - Unable to parse Sobemovirus. Name of type virus unparsable: Sobemovirus
2014-06-20 01:51:25,310 WARN : [ALANameSearcher] - Unable to parse Soil-borne wheat mosaic (Furovirus). Name of type virus unparsable: Soil-borne wheat mosaic (Furovirus)
2014-06-20 01:51:25,322 WARN : [ALANameSearcher] - Unable to parse Sorghum Mosaic Virus (Potyvirus). Name of type virus unparsable: Sorghum Mosaic Virus (Potyvirus)
2014-06-20 01:51:25,322 WARN : [ALANameSearcher] - Unable to parse Sorghum mosaic (Potyvirus). Name of type virus unparsable: Sorghum mosaic (Potyvirus)
2014-06-20 01:51:25,323 WARN : [ALANameSearcher] - Unable to parse Sour cherry green ring mottle (Closterovirus). Name of type virus unparsable: Sour cherry green ring mottle (Closterovirus)
2014-06-20 01:51:25,359 WARN : [ALANameSearcher] - Unable to parse Squash leaf curl (Begomovirus). Name of type virus unparsable: Squash leaf curl (Begomovirus)
2014-06-20 01:51:25,381 WARN : [ALANameSearcher] - Unable to parse Strawberry latent C (Rhabdovirus). Name of type virus unparsable: Strawberry latent C (Rhabdovirus)
2014-06-20 01:51:25,382 WARN : [ALANameSearcher] - Unable to parse Strawberry latent ringspot (Nepovirus). Name of type virus unparsable: Strawberry latent ringspot (Nepovirus)
2014-06-20 01:51:25,419 WARN : [ALANameSearcher] - Unable to parse Sugarcane Mosaic Virus (Potyvirus). Name of type virus unparsable: Sugarcane Mosaic Virus (Potyvirus)
2014-06-20 01:51:25,420 WARN : [ALANameSearcher] - Unable to parse Sugarcane Streak Mosaic Virus (Potyvirus). Name of type virus unparsable: Sugarcane Streak Mosaic Virus (Potyvirus)
2014-06-20 01:51:25,420 WARN : [ALANameSearcher] - Unable to parse Sugarcane Streak Virus (Mastrevirus). Name of type virus unparsable: Sugarcane Streak Virus (Mastrevirus)
2014-06-20 01:51:25,421 WARN : [ALANameSearcher] - Unable to parse Sugarcane streak mosaic (Unassigned). Name of type blacklisted unparsable: Sugarcane streak mosaic (Unassigned)
2014-06-20 01:51:25,423 WARN : [ALANameSearcher] - Unable to parse Sunflower mosaic (Potyvirus). Name of type virus unparsable: Sunflower mosaic (Potyvirus)
2014-06-20 01:51:25,423 WARN : [ALANameSearcher] - Unable to parse Sunflower yellow blotch (Umbravirus). Name of type virus unparsable: Sunflower yellow blotch (Umbravirus)
2014-06-20 01:51:25,434 WARN : [ALANameSearcher] - Unable to parse Sweet potato leaf curl (Begomovirus). Name of type virus unparsable: Sweet potato leaf curl (Begomovirus)
2014-06-20 01:51:25,527 WARN : [ALANameSearcher] - Unable to parse Thomasia purpurea x solanacea. Name of type hybrid unparsable: Thomasia purpurea x solanacea
2014-06-20 01:51:25,574 WARN : [ALANameSearcher] - Unable to parse Tobacco etch (Potyvirus). Name of type virus unparsable: Tobacco etch (Potyvirus)
2014-06-20 01:51:25,575 WARN : [ALANameSearcher] - Unable to parse Tobacco leaf curl (Bigeminivirus). Name of type virus unparsable: Tobacco leaf curl (Bigeminivirus)
2014-06-20 01:51:25,577 WARN : [ALANameSearcher] - Unable to parse Tobacco rattle (Tobravirus) (exotic strains). Name of type virus unparsable: Tobacco rattle (Tobravirus) (exotic strains)
2014-06-20 01:51:25,578 WARN : [ALANameSearcher] - Unable to parse Tobacco ringspot (Nepovirus). Name of type virus unparsable: Tobacco ringspot (Nepovirus)
2014-06-20 01:51:25,580 WARN : [ALANameSearcher] - Unable to parse Tomato black ring nepovirus. Name of type virus unparsable: Tomato black ring nepovirus
2014-06-20 01:51:25,580 WARN : [ALANameSearcher] - Unable to parse Tomato black ring (Nepovirus). Name of type virus unparsable: Tomato black ring (Nepovirus)
2014-06-20 01:51:25,581 WARN : [ALANameSearcher] - Unable to parse Tomato black ring (Nepovirus). Name of type virus unparsable: Tomato black ring (Nepovirus)
2014-06-20 01:51:25,581 WARN : [ALANameSearcher] - Unable to parse Tomato blackring (Nepovirus). Name of type virus unparsable: Tomato blackring (Nepovirus)
2014-06-20 01:51:25,582 WARN : [ALANameSearcher] - Unable to parse Tomato blackring (Nepovirus). Name of type virus unparsable: Tomato blackring (Nepovirus)
2014-06-20 01:51:25,583 WARN : [ALANameSearcher] - Unable to parse Tomato bushy stunt (Tombusvirus). Name of type virus unparsable: Tomato bushy stunt (Tombusvirus)
2014-06-20 01:51:25,583 WARN : [ALANameSearcher] - Unable to parse Tomato ringspot (Nepovirus). Name of type virus unparsable: Tomato ringspot (Nepovirus)
2014-06-20 01:51:25,592 WARN : [ALANameSearcher] - Unable to parse Tomato ringspot (Nepovirus). Name of type virus unparsable: Tomato ringspot (Nepovirus)
2014-06-20 01:51:25,594 WARN : [ALANameSearcher] - Unable to parse Tospovirus. Name of type virus unparsable: Tospovirus
2014-06-20 01:51:25,664 WARN : [ALANameSearcher] - Unable to parse UNKNOWN. Name of type blacklisted unparsable: UNKNOWN
2014-06-20 01:51:25,665 WARN : [ALANameSearcher] - Unable to parse UNKNOWN. Name of type blacklisted unparsable: UNKNOWN
2014-06-20 01:51:25,665 WARN : [ALANameSearcher] - Unable to parse UNKNOWN. Name of type blacklisted unparsable: UNKNOWN
2014-06-20 01:51:25,667 WARN : [ALANameSearcher] - Unable to parse Unassigned family, Potexvirus, Potato Virus X. Name of type blacklisted unparsable: Unassigned family, Potexvirus, Potato Virus X
2014-06-20 01:51:25,668 WARN : [ALANameSearcher] - Unable to parse Unassigned family, Tobravirus, Tobacco Rattle Virus. Syn. Potato stem mottle. Name of type blacklisted unparsable: Unassigned family, Tobravirus, Tobacco Rattle Virus. Syn. Potato stem mottle
2014-06-20 01:51:25,670 WARN : [ALANameSearcher] - Unable to parse Unassigned family,: Pomovirus; Potato mop-top. Name of type blacklisted unparsable: Unassigned family,: Pomovirus; Potato mop-top
2014-06-20 01:51:25,670 WARN : [ALANameSearcher] - Unable to parse Undetermined. Name of type blacklisted unparsable: Undetermined
2014-06-20 01:51:25,671 WARN : [ALANameSearcher] - Unable to parse Unknown. Name of type blacklisted unparsable: Unknown
2014-06-20 01:51:25,671 WARN : [ALANameSearcher] - Unable to parse Unknown. Name of type blacklisted unparsable: Unknown
2014-06-20 01:51:25,672 WARN : [ALANameSearcher] - Unable to parse Unknown. Name of type blacklisted unparsable: Unknown
2014-06-20 01:51:25,672 WARN : [ALANameSearcher] - Unable to parse Unknown etiology. Name of type blacklisted unparsable: Unknown etiology
2014-06-20 01:51:25,719 WARN : [ALANameSearcher] - Unable to parse Virus-like Impietratura (Unknown). Name of type blacklisted unparsable: Virus-like Impietratura (Unknown)
2014-06-20 01:51:25,724 WARN : [ALANameSearcher] - Unable to parse Watermelon silver mottle (Tospovirus), Groundnut bud necrosis (Tospovirus), watermelon bud necrosis (Tospovirus). Name of type virus unparsable: Watermelon silver mottle (Tospovirus), Groundnut bud necrosis (Tospovirus), watermelon bud necrosis (Tospovirus)
2014-06-20 01:51:25,726 WARN : [ALANameSearcher] - Unable to parse Welsh onion yellow stripe potyvirus. Name of type virus unparsable: Welsh onion yellow stripe potyvirus
2014-06-20 01:51:25,727 WARN : [ALANameSearcher] - Unable to parse Western X Virginia grapevine yellows III (NAGYIII). Name of type hybrid unparsable: Western X Virginia grapevine yellows III (NAGYIII)
2014-06-20 01:51:25,730 WARN : [ALANameSearcher] - Unable to parse Wheat dwarf (Mastrevirus). Name of type virus unparsable: Wheat dwarf (Mastrevirus)
2014-06-20 01:51:25,730 WARN : [ALANameSearcher] - Unable to parse Wheat spindle streak mosaic (Bymovirus). Name of type virus unparsable: Wheat spindle streak mosaic (Bymovirus)
2014-06-20 01:51:25,731 WARN : [ALANameSearcher] - Unable to parse Wheat yellow leaf (Closterovirus). Name of type virus unparsable: Wheat yellow leaf (Closterovirus)
2014-06-20 01:51:25,731 WARN : [ALANameSearcher] - Unable to parse Wheat yellow mosaic (Bymovirus). Name of type virus unparsable: Wheat yellow mosaic (Bymovirus)
2014-06-20 01:51:25,737 WARN : [ALANameSearcher] - Unable to parse X-disease phytoplasma. Name of type unkown unparsable: X-disease phytoplasma
2014-06-20 01:51:25,768 WARN : [ALANameSearcher] - Unable to parse Zucchini lethal chlorosis (Tospovirus). Name of type virus unparsable: Zucchini lethal chlorosis (Tospovirus)
2014-06-20 01:51:25,771 WARN : [ALANameSearcher] - Unable to parse e.g, Pseudococcus calceolariae, Planococcus mali. Name of type unkown unparsable: e.g, Pseudococcus calceolariae, Planococcus mali
2014-06-20 01:51:26,016 INFO : [Consumer] - Killing (Actor.act) thread: 0
----------------------------------------------------------------------------------------------------------------------------------------------------------------
biocache> index dr0
2014-06-20 01:54:06,289 INFO : [IndexRecords] - Starting to index dr0| until dr0|~
2014-06-20 01:54:06,609 INFO : [TaxonSpeciesListDAO] - Updating the lists
2014-06-20 01:54:07,474 INFO : [TaxonSpeciesListDAO] - The number of distinct species 0
2014-06-20 01:54:07,477 INFO : [TaxonSpeciesListDAO] - Finished creating the map
2014-06-20 01:54:07,505 INFO : [IndexRecords] - Total indexing time 1.214 seconds
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.
More information about the Ala-portal
mailing list