<div dir="ltr">Thanks David,<div><br></div><div>We will check these files.</div><div><br></div><div>Regards,</div><div><br></div><div><div dir="ltr" style="font-family:arial,sans-serif;font-size:13px"><div class="im"><div class="gmail_extra" style="color:rgb(136,136,136)">
Daniel Lins da Silva</div><div class="gmail_extra" style="color:rgb(136,136,136)">(Mobile) <a href="tel:55%2011%2096144-4050" value="+5511961444050" target="_blank">55 11 96144-4050</a></div><div style="color:rgb(136,136,136)">
<div class="gmail_extra"><font color="#000000">Research Center <span id="3ed6651d-2492-4602-a140-7d0731cc886a" class="GINGER_SOFTWARE_mark">on</span> Biodiversity and Computing (Biocomp)</font></div><div class="gmail_extra">
<font color="#000000">University of Sao Paulo, Brazil</font></div></div><div class="gmail_extra" style="color:rgb(136,136,136)"><a href="mailto:daniellins@usp.br" target="_blank">daniellins@usp.br</a></div><div class="gmail_extra" style="color:rgb(136,136,136)">
<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a></div><div><br></div></div></div></div><div><br></div><div>Daniel.</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-27 1:31 GMT-03:00  <span dir="ltr">&lt;<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a>&gt;</span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">




<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">
<div style="direction:ltr">
<div style="direction:ltr">
<div style="direction:ltr">Thanks for resending Pedro.</div>
<div style="direction:ltr"><br>
</div>
<div style="direction:ltr">We are recommending using the Ansible scripts [1] for installation of components. </div>
<div style="direction:ltr">If this isn&#39;t possible, its worth checking out the templates in use by these scripts [2].</div>
<div style="direction:ltr">There is a property at the bottom of this file that disables the API key check.</div>
<div style="direction:ltr"><br>
</div>
<div style="direction:ltr">security.apikey.checkEnabled=false</div>
<div style="direction:ltr"><br>
</div>
<div style="direction:ltr">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.</div>
<div style="direction:ltr">It&#39;s worth checking to see if the ports are open between these machines.</div>
<div style="direction:ltr"><br>
</div>
<div style="direction:ltr">Cheers</div>
<div style="direction:ltr"><br>
</div>
<div style="direction:ltr">Dave</div>
<div style="direction:ltr"><br>
</div>
<div style="direction:ltr">[1] <a href="https://github.com/gbif/ala-install/blob/master/ansible/roles/collectory/templates/config/collectory-config.properties" style="font-size:10pt" target="_blank">https://github.com/gbif/ala-install</a></div>

<div style="direction:ltr">[2] <a href="https://github.com/gbif/ala-install/blob/master/ansible/roles/collectory/templates/config/collectory-config.properties" style="font-size:10pt" target="_blank">https://github.com/gbif/ala-install/blob/master/ansible/roles/collectory/templates/config/collectory-config.properties</a></div>

<div style="direction:ltr"><br>
</div>
</div>
</div>
<div>
<div style="direction:ltr">
<div>
<div style="color:rgb(0,0,0);font-family:Tahoma;font-size:10pt">
<div style="font-family:Times New Roman;color:#000000;font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> Daniel Lins [<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>]<br>
<b>Sent:</b> 27 June 2014 13:54<br>
<b>To:</b> Martin, Dave (CES, Black Mountain)<br>
<b>Cc:</b> <a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a>; Pedro Corrêa<br>
<b>Subject:</b> Re: [Ala-portal] DwC-A loading problems<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">Hi Dave,
<div><br>
<div>Did you see this mail? Do you think this issue can be something related to the configuration of api_key property?<br>
</div>
</div>
<div><br>
</div>
<div>Thanks.</div>
<div><br>
</div>
<div>Regards,</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2014-06-25 2:14 GMT-03:00 Daniel Lins <span dir="ltr">&lt;<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>&gt;</span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Dave, 
<div><br>
</div>
<div>Thanks for the support.</div>
<div><br>
</div>
<div>The data loading in the biocache is working properly now. But error continues during the update of
<span>collectory</span> (see below).<br>
</div>
<div><br>
</div>
<div>
<div><i>java.net.SocketTimeoutException: Read timed out</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun<span>.</span>reflect<span>.</span>NativeConstructorAccessorImpl<span>.</span>newInstance0<span>(</span>Native Method)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun<span>.</span>reflect<span>.</span>NativeConstructorAccessorImpl<span>.</span><span>newInstance</span><span>(</span>NativeConstructorAccessorImpl.java<span>:</span>57)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span>at</span> sun<span>.</span>reflect<span>.</span>DelegatingConstructorAccessorImpl<span>.</span><span>newInstance</span><span>(</span>DelegatingConstructorAccessorImpl.java<span>:</span>45)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span><span>lang</span><span>.</span>reflect<span>.</span>Constructor<span>.</span><span>newInstance</span><span>(</span>Constructor.java<span>:</span>526)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1675)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1673)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span>security<span>.</span><span>AccessController</span><span>.</span><span>doPrivileged</span><span>(</span>Native Method)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1671)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1244)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scalaj</span><span>.</span>http<span>.</span>Http$Request<span>.</span>liftedTree1$1<span>(</span>Http<span>.</span><span>scala</span><span>:</span>107)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> scalaj.http.Http$Request.process(Http.scala:103)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scalaj</span><span>.</span>http<span>.</span>Http$Request<span>.</span><span>responseCode</span><span>(</span>Http<span>.</span><span>scala</span><span>:</span>120)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.load.DataLoader$class.updateLastChecked(DataLoader.scala:354)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.load.DwCALoader.updateLastChecked(DwCALoader.scala:74)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.load.DwCALoader.load(DwCALoader.scala:103)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.load.Loader.load(Loader.scala:75)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.cmd.CMD$$anonfun$executeCommand$7.apply(CMD.scala:69)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.cmd.CMD$$anonfun$executeCommand$7.apply(CMD.scala:69)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scala</span><span>.</span>collection<span>.</span>IndexedSeqOptimized$class<span>.</span><span>foreach</span><span>(</span>IndexedSeqOptimized<span>.</span><span>scala</span><span>:</span>33)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scala</span><span>.</span>collection<span>.</span>mutable<span>.</span>ArrayOps$ofRef<span>.</span><span>foreach</span><span>(</span>ArrayOps<span>.</span><span>scala</span><span>:</span>108)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span>a</span><span>t</span>
 au.org.ala.biocache.cmd.CMD$.executeCommand(CMD.scala:69)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.cmd.CommandLineTool$.main(CommandLineTool.scala:22)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.cmd.CommandLineTool.main(CommandLineTool.scala)</i></div>
<div><i>Caused by: java.net.SocketTimeoutException: Read timed out</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.SocketInputStream.socketRead0(Native Method)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.SocketInputStream.read(SocketInputStream.java:152)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.SocketInputStream.read(SocketInputStream.java:122)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span><span>io</span><span>.</span>BufferedInputStream<span>.</span>fill<span>(</span>BufferedInputStream.java<span>:</span>235)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span><span>io</span><span>.</span>BufferedInputStream<span>.</span>read1<span>(</span>BufferedInputStream.java<span>:</span>275)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span><span>io</span><span>.</span>BufferedInputStream<span>.</span>read<span>(</span>BufferedInputStream.java<span>:</span>334)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:687)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:633)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1323)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scalaj</span><span>.</span>http<span>.</span>Http$Request$$anonfun$responseCode$1<span>.</span>apply<span>(</span>Http<span>.</span><span>scala</span><span>:</span>120)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span style="white-space:pre-wrap"></span><span>atscala</span>
<span><span>j</span>.</span>htt<span>p</span><span>.</span>Http$Request$$anonfun$responseCode$<span>1</span><span>.</span><span>appl<span>y</span></span><span>(</span>Htt<span>p</span><span>.</span><span>scal<span>a</span></span><span>:</span>120)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scalaj</span><span>.</span>http<span>.</span>Http$Request<span>.</span>liftedTree1$1<span>(</span>Http<span>.</span><span>scala</span><span>:</span>104)</i></div>

<div><i><span style="white-space:pre-wrap"></span>... 13 more</i></div>
</div>
<div><br>
</div>
<div>In the external configuration file (/data/biocache/config/biocache-config.properties) the property registry<span>.</span>url is correct (registry<span>.</span>url=http<span>:</span>//<a href="http://192.168.15.132:8080/" target="_blank">192.168.15.132:8080/</a><span>collectory</span>/<span>ws</span>), indicating
 the URL of the <span>collectory</span> WS page.</div>
<div><br>
</div>
<div>It could be something related to permission for external access? How works this
<b>api_key</b> property in the <span>collectory</span>?<br>
</div>
<div><br>
</div>
<div>Thanks!</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
Daniel Lins da Silva</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
(Mobile) <a href="tel:55%2011%2096144-4050" value="+5511961444050" target="_blank">55 11 96144-4050</a></div>
<div style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<div class="gmail_extra"><font color="#000000">Research Center <span>on</span> Biodiversity and Computing (Biocomp)</font></div>
<div class="gmail_extra"><font color="#000000">University of Sao Paulo, Brazil</font></div>
</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<a href="mailto:daniellins@usp.br" target="_blank">daniellins@usp.br</a></div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a></div>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2014-06-20 2:26 GMT-03:00 <span dir="ltr">&lt;<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a>&gt;</span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Hi Daniel.
<div><br>
</div>
<div>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).</div>

<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div>&gt;&gt; truncate occ;</div>
<div><br>
</div>
<div>This will remove all occurrence records from the database, but not from the index. </div>
<div><br>
</div>
<div>The warnings you are seeing in the processing phase e.g.</div>
<div><br>
</div>
<div><i style="font-family:&#39;Times New Roman&#39;;font-size:16px">2014-06-20 01:51:20,505 WARN<span> :</span> [ALANameSearcher] - Unable to parse Abaca bunchy top  (Babuvirus). Name of type virus <span>unparsable</span>: Abaca bunchy top  (Babuvirus)</i></div>

<div><i style="font-family:&#39;Times New Roman&#39;;font-size:16px"><br>
</i></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px">are normal. This is referring to the sensitive species list in use.</span></div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
Dave</div>
<div><br>
</div>
<div><br>
<div style="font-family:Times New Roman;color:#000000;font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> Daniel Lins [<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>]<br>
<b>Sent:</b> 20 June 2014 15:11<br>
<b>To:</b> Martin, Dave (CES, Black Mountain)<br>
<b>Cc:</b> <a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a>; dos Remedios, Nick (CES, Black Mountain); Pedro Corrêa<br>
<b>Subject:</b> Re: [Ala-portal] DwC-A loading problems<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">Hi Dave, thanks for the information from the last email.
<div><br>
</div>
<div>I&#39;m following your advice and performing the update of our test environment for biocache version 1.1. But I&#39;m having some problems and I would like to know if you or anyone has already found this issue and know a solution.</div>

<div><br>
</div>
<div>To update the biocache version I did these steps below (based on the Vagrant/Ansible installation process):<br>
</div>
<div><br>
</div>
<div>
<div>1. Cleaning of the database and index through <span>delete</span>-resource function (delete-resource dr0 dr1 dr2<span> ...</span>);</div>
<div>2. An update of the Biocache config file (/data/biocache/config/biocache-config.properties) (copied from the Vagrant VM, with some configuration changes);</div>
<div>3. An update of the biocache build file (biocache. <span>jar</span>) (copied from the Vagrant VM - /usr/lib/biocache);</div>
<div>4. Deployment of the new biocache-service build (copied from the Vagrant VM - tomcat7/<span>webapps</span>/biocache-service<span>.</span>war)</div>
<div>5. An update of the Solr config files (schema.xml, solrconfig.xml) (copied from the Vagrant VM - /data/<span>solr</span>/biocache);</div>
<div>6. Exclusion of the indexing folder of Biocache Core (/data/<span>solr</span>/biocache/data);</div>
<div><br>
</div>
<div>Notes 1 ** No change was made in the Hubs-<span>Webapp</span> and Collectory.</div>
</div>
<div><br>
</div>
<div>Notes 2 **  The import of CSV files is working (using load-local-<span>csv</span> dr0 /&lt;file_location&gt;/xxx.csv). </div>
<div><br>
</div>
<div><br>
</div>
<div>I tried to import a Darwin Core Archive by following these steps:<br>
</div>
<div><br>
</div>
<div>1. Created a data resource (dr0);</div>
<div><br>
</div>
<div>2. Uploaded a DWC-A zip file into the DR using the &quot;Upload File&quot; option.</div>
<div><br>
</div>
<div>
<div><i>Protocol<span>:</span>DarwinCore archive</i></div>
<div><i>Location URL<span>:</span>file<span>:</span>////data/<span>collectory</span>/upload/1403239521145/dwca-ocorrencias_lobo_guara_1<span>.</span>zip</i></div>
<div><i>Automatically loaded<span>:</span>false</i></div>
<div><i><span>DwC</span> terms that uniquely identify a record: <span>occurrenceID</span></i></div>
<div><i>Strip <span>whitespaces</span> in key: false</i></div>
<div><i>Incremental Load: false</i></div>
</div>
<div><br>
</div>
<div>3. Used the Command Line Tool (Biocache) to Load (<i>load dr0</i>), Process (<i>process dr0</i>) and Index (<i>index dr0</i>) data.</div>
<div><br>
</div>
<div><br>
</div>
<div>During the data loading phase, the system generated these errors:</div>
<div><br>
</div>
<div><i>...</i></div>
<div>
<div><i>2014-06-20 01:49:12,506 INFO<span> :</span> [<span>DataLoader</span>] - Finished DwC loader. Records processed: 32</i></div>
<div><i>java.net.SocketTimeoutException: Read timed out</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun<span>.</span>reflect<span>.</span>NativeConstructorAccessorImpl<span>.</span>newInstance0<span>(</span>Native Method)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun<span>.</span>reflect<span>.</span>NativeConstructorAccessorImpl<span>.</span><span>newInstance</span><span>(</span>NativeConstructorAccessorImpl.java<span>:</span>57)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun<span>.</span>reflect<span>.</span>DelegatingConstructorAccessorImpl<span>.</span><span>newInstance</span><span>(</span>DelegatingConstructorAccessorImpl.java<span>:</span>45)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span><span>lang</span><span>.</span>reflect<span>.</span>Constructor<span>.</span><span>newInstance</span><span>(</span>Constructor.java<span>:</span>526)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1675)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1673)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span>security<span>.</span><span>AccessController</span><span>.</span><span>doPrivileged</span><span>(</span>Native Method)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1671)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1244)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scalaj</span><span>.</span>http<span>.</span>Http$Request<span>.</span>liftedTree1$1<span>(</span>Http<span>.</span><span>scala</span><span>:</span>107)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> scalaj.http.Http$Request.process(Http.scala:103)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scalaj</span><span>.</span>http<span>.</span>Http$Request<span>.</span><span>responseCode</span><span>(</span>Http<span>.</span><span>scala</span><span>:</span>120)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.load.DataLoader$class.updateLastChecked(DataLoader.scala:354)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.load.DwCALoader.updateLastChecked(DwCALoader.scala:74)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.load.DwCALoader.load(DwCALoader.scala:103)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.load.Loader.load(Loader.scala:75)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.cmd.CMD$$anonfun$executeCommand$7.apply(CMD.scala:69)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.cmd.CMD$$anonfun$executeCommand$7.apply(CMD.scala:69)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scala</span><span>.</span>collection<span>.</span>IndexedSeqOptimized$class<span>.</span><span>foreach</span><span>(</span>IndexedSeqOptimized<span>.</span><span>scala</span><span>:</span>33)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scala</span><span>.</span>collection<span>.</span>mutable<span>.</span>ArrayOps$ofRef<span>.</span><span>foreach</span><span>(</span>ArrayOps<span>.</span><span>scala</span><span>:</span>108)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.cmd.CMD$.executeCommand(CMD.scala:69)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.cmd.CommandLineTool$.main(CommandLineTool.scala:22)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> au.org.ala.biocache.cmd.CommandLineTool.main(CommandLineTool.scala)</i></div>
<div><i>Caused by: java.net.SocketTimeoutException: Read timed out</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.SocketInputStream.socketRead0(Native Method)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.SocketInputStream.read(SocketInputStream.java:152)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.SocketInputStream.read(SocketInputStream.java:122)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span><span>io</span><span>.</span>BufferedInputStream<span>.</span>fill<span>(</span>BufferedInputStream.java<span>:</span>235)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span><span>io</span><span>.</span>BufferedInputStream<span>.</span>read1<span>(</span>BufferedInputStream.java<span>:</span>275)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>java</span><span>.</span><span>io</span><span>.</span>BufferedInputStream<span>.</span>read<span>(</span>BufferedInputStream.java<span>:</span>334)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:687)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:633)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1323)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468)</i></div>
<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scalaj</span><span>.</span>http<span>.</span>Http$Request$$anonfun$responseCode$1<span>.</span>apply<span>(</span>Http<span>.</span><span>scala</span><span>:</span>120)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scalaj</span><span>.</span>http<span>.</span>Http$Request$$anonfun$responseCode$1<span>.</span>apply<span>(</span>Http<span>.</span><span>scala</span><span>:</span>120)</i></div>

<div><i><span style="white-space:pre-wrap"></span><span>at</span> <span>scalaj</span><span>.</span>http<span>.</span>Http$Request<span>.</span>liftedTree1$1<span>(</span>Http<span>.</span><span>scala</span><span>:</span>104)</i></div>

<div><i><span style="white-space:pre-wrap"></span>... 13 more</i></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>And in Cassandra was saved only one record:<br>
</div>
<div><br>
</div>
<div>
<div><i><span>cqlsh</span><span>:</span><span>occ</span>&gt; select * from <span>occ</span>;<br>
</i></div>
<div><i><br>
</i></div>
<div><i> <span>key</span>      | <span>portalId</span> | <span>uuid</span></i></div>
<div><i>----------+----------+--------------------------------------</i></div>
<div><i> dr0|null |     null | 1b5b21fc-594a-46e6-b8db-cf37c50b8f7b</i></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>During the data processing phase, the system generated these additional errors:</div>
</div>
<div><br>
</div>
<div>...</div>
<div>
<div><i>Jun 20, 2014 1:51:08 AM org<span>.</span><span>geotools</span><span>.</span>referencing<span>.</span>factory<span>.</span><span>epsg</span><span>.</span>ThreadedHsqlEpsgFactory
<span>createDataSource</span></i></div>
<div><i>INFO: Building new data source for org<span>.</span><span>geotools</span><span>.</span>referencing<span>.</span>factory<span>.</span><span>epsg</span><span>.</span>ThreadedHsqlEpsgFactory</i></div>
<div><i>Jun 20, 2014 1:51:08 AM org<span>.</span><span>geotools</span><span>.</span>referencing<span>.</span>factory<span>.</span><span>epsg</span><span>.</span>ThreadedHsqlEpsgFactory
<span>createBackingStore</span></i></div>
<div><i>INFO: Building backing store for org<span>.</span><span>geotools</span><span>.</span>referencing<span>.</span>factory<span>.</span><span>epsg</span><span>.</span>ThreadedHsqlEpsgFactory</i></div>
<div><i>2014-06-20 01:51:20,505 WARN<span> :</span> [ALANameSearcher] - Unable to parse Abaca bunchy top  (Babuvirus). Name of type virus
<span>unparsable</span>: Abaca bunchy top  (Babuvirus)</i></div>
<div><i>2014-06-20 01:51:20,509 WARN<span> :</span> [ALANameSearcher] - Unable to parse Abaca mosaic, sugarcane mosaic (Potyvirus). Name of type virus
<span>unparsable</span>: Abaca mosaic, sugarcane mosaic (Potyvirus)</i></div>
<div><i>2014-06-20 01:51:21,210 WARN<span> :</span> [ALANameSearcher] - Unable to parse Acute bee paralysis  (Cripavirus). Name of type virus
<span>unparsable</span>: Acute bee paralysis  (Cripavirus)</i></div>
<div><i>2014-06-20 01:51:21,255 WARN<span> :</span> [ALANameSearcher] - Unable to parse Agropyron mosaic  (Rymovirus). Name of type virus
<span>unparsable</span>: Agropyron mosaic  (Rymovirus)</i></div>
<div><i>2014-06-20 01:51:21,289 WARN<span> :</span> [ALANameSearcher] - Unable to parse Alphacrytovirus
<span>vicia</span>. Name of type virus <span>unparsable</span>: Alphacrytovirus <span>
vicia</span></i></div>
<div><i>2014-06-20 01:51:21,334 WARN<span> :</span> [ALANameSearcher] - Unable to parse American plum line pattern  (APLPV, Ilaravirus). Name of type virus
<span>unparsable</span>: American plum line pattern  (APLPV, Ilaravirus)</i></div>
<div><i>2014-06-20 01:51:21,525 WARN<span> :</span> [ALANameSearcher] - Unable to parse Apis iridescent  (Iridovirus). Name of type virus
<span>unparsable</span>: Apis iridescent  (Iridovirus)</i></div>
<div><i>2014-06-20 01:51:21,546 WARN<span> :</span> [ALANameSearcher] - Unable to parse Apricot ring pox  (Unassigned).
<span>Name</span> of type blacklisted <span>unparsable</span>: Apricot ring pox  (Unassigned)</i></div>
<div><i>2014-06-20 01:51:21,549 WARN<span> :</span> [ALANameSearcher] - Unable to parse Arabis mosaic  (Nepovirus). Name of type virus
<span>unparsable</span>: Arabis mosaic  (Nepovirus)</i></div>
<div><i>2014-06-20 01:51:21,623 WARN<span> :</span> [ALANameSearcher] - Unable to parse Artichoke Italian latent  (Nepovirus). Name of type virus
<span>unparsable</span>: Artichoke Italian latent  (Nepovirus)</i></div>
<div><i>2014-06-20 01:51:21,640 WARN<span> :</span> [ALANameSearcher] - Unable to parse Asparagus   (Ilarvirus). Name of type virus
<span>unparsable</span>: Asparagus   (Ilarvirus)</i></div>
<div><i>2014-06-20 01:51:21,641 WARN<span> :</span> [ALANameSearcher] - Unable to parse Asparagus   (Potyvirus). Name of type virus
<span>unparsable</span>: Asparagus   (Potyvirus)</i></div>
</div>
<div>...</div>
<div><br>
</div>
<div>During the last <span>phase there</span> were no errors. However, only one record was indexed.<br>
</div>
<div><br>
</div>
<div>
<div><i>2014-06-20 01:54:07,739 INFO<span> :</span> [SolrIndexDAO] - &gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt; Document count of index: 1</i></div>
<div><i>2014-06-20 01:54:07,741 INFO<span> :</span> [SolrIndexDAO] - <span>Finalise</span> finished.</i></div>
</div>
<div><i><br>
</i></div>
<div>
<div>I attached a file with the complete messages generated by Biocache during this test.</div>
<div style="font-style:italic"><br>
</div>
</div>
<div><i><br>
</i></div>
<div>Thanks!</div>
<div><br>
</div>
<div>Cheers.</div>
<div><br>
</div>
<div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
Daniel Lins da Silva</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
(Mobile) <a href="tel:55%2011%2096144-4050" value="+5511961444050" target="_blank">55 11 96144-4050</a></div>
<div style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<div class="gmail_extra"><font color="#000000">Research Center <span>on</span> Biodiversity and Computing (Biocomp)</font></div>
<div class="gmail_extra"><font color="#000000">University of Sao Paulo, Brazil</font></div>
</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<a href="mailto:daniellins@usp.br" target="_blank">daniellins@usp.br</a></div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a></div>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2014-06-18 6:15 GMT-03:00 <span dir="ltr">&lt;<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a>&gt;</span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">
<div>Hi Daniel,</div>
<div><br>
</div>
<div>From what you&#39;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.</div>
<div><br>
</div>
<div>We can tell you that functionally there wasn&#39;t a great deal of difference between the later snapshots of 1.0 and 1.1.</div>
<div>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.</div>
<div><br>
</div>
<div>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&#39;ll need to regenerate your index using the biocache commandline tool. Upgrading to 1.1 shouldnt
 require any changes to hubs-webapp if you&#39;ve customised this component. </div>
<div><br>
</div>
<div>I&#39;d really recommend move to 1.1 sooner rather than later as it&#39;ll give you a stable baseline to work against.</div>
<div><br>
</div>
<div>Hope this helps,</div>
<div><br>
</div>
<div>Dave Martin</div>
<div>ALA</div>
<div><br>
</div>
<div style="font-family:Times New Roman;color:#000000;font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> Daniel Lins [<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>]<br>
<b>Sent:</b> 18 June 2014 15:54
<div>
<div><br>
<b>To:</b> Martin, Dave (CES, Black Mountain)<br>
<b>Cc:</b> <a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a>; dos Remedios, Nick (CES, Black Mountain); Pedro Corrêa; Nicholls, Miles (CES, Black Mountain)<br>
<b>Subject:</b> Re: [Ala-portal] DwC-A loading problems<br>
</div>
</div>
</font><br>
</div>
<div>
<div>
<div></div>
<div>
<div dir="ltr">
<div>
<div>Hi Dave, </div>
<div><br>
</div>
<div>How can I update the Biocache-1.0-SNAPSHOT to the version 1.1? I updated the
<span>biocache-store</span> (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.</div>
<div><br>
</div>
<div>This update will generate some impacts in other components?</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Can you advise me as to the best way forward?<br>
</div>
</div>
<div><br>
</div>
<div>Thanks!!</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>
<div style="font-family:arial,sans-serif;font-size:13px">
<div class="gmail_extra" style="color:rgb(136,136,136)">Daniel Lins da Silva</div>
<div class="gmail_extra" style="color:rgb(136,136,136)">(Mobile) <a href="tel:55%2011%2096144-4050" value="+5511961444050" target="_blank">55 11 96144-4050</a></div>
<div style="color:rgb(136,136,136)">
<div class="gmail_extra"><font color="#000000">Research Center <span>on</span> Biodiversity and Computing (Biocomp)</font></div>
<div class="gmail_extra"><font color="#000000">University of Sao Paulo, Brazil</font></div>
</div>
<div class="gmail_extra" style="color:rgb(136,136,136)"><a href="mailto:daniellins@usp.br" target="_blank">daniellins@usp.br</a></div>
<div class="gmail_extra" style="color:rgb(136,136,136)"><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a></div>
<div><br>
</div>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2014-05-26 3:58 GMT-03:00 <span dir="ltr">&lt;<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a>&gt;</span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Thanks Daniel.
<div><br>
</div>
<div><span style="font-size:10pt">I&#39;d recommend upgrading to 1.1 and I&#39;d recommend installation with the ansible scripts. This will give you base line configuration.</span></div>
<div><span style="font-size:10pt">The scripts can be tested on a local machine using vagrant.</span></div>
<div><span style="font-size:10pt">The configuration between 1.0 and 1.1 changed significantly - removal of redundant, legacy properties, adoption of standard format for property names.</span></div>
<div>Heres the template used for the configuration file in the ansible scripts:</div>
<div><br>
</div>
<div><a href="https://github.com/gbif/ala-install/blob/master/ansible/roles/biocache-service/templates/config/biocache-config.properties" target="_blank">https://github.com/gbif/ala-install/blob/master/ansible/roles/biocache-service/templates/config/biocache-config.properties</a></div>

<div><br>
</div>
<div>Cheers</div>
<div><br>
</div>
<div>Dave Martin</div>
<div>ALA</div>
<div><br>
<div>
<div style="font-family:Times New Roman;color:#000000;font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> Daniel Lins [<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>]<br>
<b>Sent:</b> 26 May 2014 15:02<br>
<b>To:</b> Martin, Dave (CES, Black Mountain)<br>
<b>Cc:</b> <a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a>; dos Remedios, Nick (CES, Black Mountain); Pedro Corrêa; Nicholls, Miles (CES, Black Mountain)<br>
<b>Subject:</b> Re: [Ala-portal] DwC-A loading problems<br>
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<div dir="ltr">Hi Dave,
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<div>When I ran the ingest command (<font size="1" face="courier new, monospace">ingest dr0</font>), the system showed errors like these below. However, after the error messages, I ran the index command (<font size="1" face="courier new, monospace">index dr0</font>),
 and data were published on the Portal.<br>
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<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,412 ERROR: [Grid] - cannot find GRID: /data/<span><span><span><span><span>ala</span></span></span></span></span>/data/layers/ready/diva/worldclim_bio_19</font></div>

<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,414 ERROR: [Grid] -
<span><span><span><span><span>java</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>io</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>FileNotFoundException:
 /data/<span><span><span><span><span>ala</span></span></span></span></span>/data/layers/ready/diva/worldclim_bio_19<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>gri</span></span></span></span></span> (No such
 file or directory)</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span><span><span>at</span></span></span></span></span>
<span><span><span><span><span>java</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>io</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>RandomAccessFile<span><span><span><span><span>.</span></span></span></span></span>open<span><span><span><span><span>(</span></span></span></span></span>Native
 Method)</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span><span><span>at</span></span></span></span></span>
<span><span><span><span><span>java</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>io</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>RandomAccessFile.&lt;<span><span><span><span><span>init</span></span></span></span></span>&gt;(RandomAccessFile.java<span><span><span><span><span>:</span></span></span></span></span>241)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span><span><span>at</span></span></span></span></span>
<span><span><span><span><span>java</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>io</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>RandomAccessFile.&lt;<span><span><span><span><span>init</span></span></span></span></span>&gt;(RandomAccessFile.java<span><span><span><span><span>:</span></span></span></span></span>122)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span><span><span>at</span></span></span></span></span> org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>ala</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>layers<span><span><span><span><span>.</span></span></span></span></span>intersect<span><span><span><span><span>.</span></span></span></span></span>Grid<span><span><span><span><span>.</span></span></span></span></span>getValues3<span><span><span><span><span>(</span></span></span></span></span>Grid.java<span><span><span><span><span>:</span></span></span></span></span>1017)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span><span><span>at</span></span></span></span></span> org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>ala</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>layers<span><span><span><span><span>.</span></span></span></span></span>intersect<span><span><span><span><span>.</span></span></span></span></span>SamplingThread<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>intersectGrid</span></span></span></span></span><span><span><span><span><span>(</span></span></span></span></span>SamplingThread.java<span><span><span><span><span>:</span></span></span></span></span>112)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span><span><span>at</span></span></span></span></span> org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>ala</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>layers<span><span><span><span><span>.</span></span></span></span></span>intersect<span><span><span><span><span>.</span></span></span></span></span>SamplingThread<span><span><span><span><span>.</span></span></span></span></span>sample<span><span><span><span><span>(</span></span></span></span></span>SamplingThread.java<span><span><span><span><span>:</span></span></span></span></span>97)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span><span><span>at</span></span></span></span></span> org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>ala</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>layers<span><span><span><span><span>.</span></span></span></span></span>intersect<span><span><span><span><span>.</span></span></span></span></span>SamplingThread<span><span><span><span><span>.</span></span></span></span></span>run<span><span><span><span><span>(</span></span></span></span></span>SamplingThread.java<span><span><span><span><span>:</span></span></span></span></span>67)</font></div>

<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,447 INFO<span><span><span><span><span> :</span></span></span></span></span> [Sampling] - ********* END - TEST BATCH SAMPLING FROM FILE ***************</font></div>

<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,496 INFO<span><span><span><span><span> :</span></span></span></span></span> [Sampling] - Finished loading: /tmp/sampling-dr0<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>txt</span></span></span></span></span>
 in 49ms</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,496 INFO<span><span><span><span><span> :</span></span></span></span></span> [Sampling] - Removing temporary file: /tmp/sampling-dr0<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>txt</span></span></span></span></span></font></div>

<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,553 INFO<span><span><span><span><span> :</span></span></span></span></span> [Consumer] -
<span><span><span><span><span>Initialising</span></span></span></span></span> thread: 0</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,575 INFO<span><span><span><span><span> :</span></span></span></span></span> [Consumer] -
<span><span><span><span><span>Initialising</span></span></span></span></span> thread: 1</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,575 INFO<span><span><span><span><span> :</span></span></span></span></span> [Consumer] -
<span><span><span><span><span>Initialising</span></span></span></span></span> thread: 2</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,577 INFO<span><span><span><span> :</span></span></span></span> [Consumer] - In thread: 0</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,579 INFO<span><span><span><span> :</span></span></span></span> [Consumer] -
<span><span><span><span>Initialising</span></span></span></span> thread: 3</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,579 INFO<span><span><span><span> :</span></span></span></span> [ProcessWithActors] - Starting with dr0|
<span><span><span><span>endingwith</span></span></span></span> dr0|~</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,581 INFO<span><span><span><span> :</span></span></span></span> [Consumer] - In thread: 2</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,581 INFO<span><span><span><span> :</span></span></span></span> [Consumer] - In thread: 1</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,584 INFO<span><span><span><span> :</span></span></span></span> [Consumer] - In thread: 3</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,592 INFO<span><span><span><span> :</span></span></span></span> [ProcessWithActors] -
<span><span><span><span>Initialised</span></span></span></span> actors...</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,647 INFO<span><span><span><span> :</span></span></span></span> [ProcessWithActors] - First
<span><span><span><span>rowKey</span></span></span></span> processed: dr0|urn<span><span><span><span>:</span></span></span></span><span><span><span><span>lsid</span></span></span></span><span><span><span><span>:</span></span></span></span><span><span><span><span>icmbio</span></span></span></span><span><span><span><span>.</span></span></span></span><span><span><span><span>gov</span></span></span></span><span><span><span><span>.</span></span></span></span><span><span><span><span>br</span></span></span></span><span><span><span><span>:</span></span></span></span><span><span><span><span>icmbio</span></span></span></span><span><span><span><span>.</span></span></span></span><span><span><span><span>parnaso</span></span></span></span><span><span><span><span>.</span></span></span></span>occurrence<span><span><span><span>:</span></span></span></span>MA120999</font></div>

<div><font size="1" face="courier new, monospace">2014-05-20 14:15:05,998 INFO<span><span><span><span> :</span></span></span></span> [ProcessWithActors] - Last row key processed: dr0|urn<span><span><span><span>:</span></span></span></span><span><span><span><span>lsid</span></span></span></span><span><span><span><span>:</span></span></span></span><span><span><span><span>icmbio</span></span></span></span><span><span><span><span>.</span></span></span></span><span><span><span><span>gov</span></span></span></span><span><span><span><span>.</span></span></span></span><span><span><span><span>br</span></span></span></span><span><span><span><span>:</span></span></span></span><span><span><span><span>icmbio</span></span></span></span><span><span><span><span>.</span></span></span></span><span><span><span><span>parnaso</span></span></span></span><span><span><span><span>.</span></span></span></span>occurrence<span><span><span><span>:</span></span></span></span>MA99991</font></div>

<div><font size="1" face="courier new, monospace">2014-05-20 14:15:06,006 INFO<span><span><span><span> :</span></span></span></span> [ProcessWithActors] - Finished.</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:06,015 INFO<span><span><span><span> :</span></span></span></span> [AttributionDAO] - Calling web service for dr0</font></div>
<div><font size="1" face="courier new, monospace">2014-05-20 14:15:06,017 INFO<span><span><span><span> :</span></span></span></span> [Consumer] - Killing (Actor<span><span><span><span>.</span></span></span></span>act) thread: 3</font></div>

<div><font size="1" face="courier new, monospace">2014-05-20 14:15:06,016 INFO<span><span><span><span> :</span></span></span></span> [Consumer] - Killing (Actor<span><span><span><span>.</span></span></span></span>act) thread: 2</font></div>

<div><font size="1" face="courier new, monospace">2014-05-20 14:15:06,015 INFO<span><span><span><span> :</span></span></span></span> [Consumer] - Killing (Actor<span><span><span><span>.</span></span></span></span>act) thread: 1</font></div>

<div><font size="1" face="courier new, monospace">2014-05-20 14:15:06,289 INFO<span><span><span><span> :</span></span></span></span> [AttributionDAO] - Looking up
<span><span><span><span>collectory</span></span></span></span> web service for ICMBIO|PARNASO</font></div>
<div><font size="1" face="courier new, monospace">May 20, 2014 2:15:10 PM org<span><span><span><span>.</span></span></span></span><span><span><span><span>geotools</span></span></span></span><span><span><span><span>.</span></span></span></span>referencing<span><span><span><span>.</span></span></span></span>factory<span><span><span><span>.</span></span></span></span><span><span><span><span>epsg</span></span></span></span><span><span><span><span>.</span></span></span></span>ThreadedEpsgFactory
 &lt;<span><span><span><span>init</span></span></span></span>&gt;</font></div>
<div><font size="1" face="courier new, monospace">INFO: Setting the EPSG factory org<span><span><span><span>.</span></span></span></span><span><span><span><span>geotools</span></span></span></span><span><span><span><span>.</span></span></span></span>referencing<span><span><span><span>.</span></span></span></span>factory<span><span><span><span>.</span></span></span></span><span><span><span><span>epsg</span></span></span></span><span><span><span><span>.</span></span></span></span>DefaultFactory
 to a 1800000ms timeout</font></div>
<div><font size="1" face="courier new, monospace">May 20, 2014 2:15:10 PM org<span><span><span><span>.</span></span></span></span><span><span><span><span>geotools</span></span></span></span><span><span><span><span>.</span></span></span></span>referencing<span><span><span><span>.</span></span></span></span>factory<span><span><span><span>.</span></span></span></span><span><span><span><span>epsg</span></span></span></span><span><span><span><span>.</span></span></span></span>ThreadedEpsgFactory
 &lt;<span><span><span><span>init</span></span></span></span>&gt;</font></div>
<div><font size="1" face="courier new, monospace">INFO: Setting the EPSG factory org<span><span><span><span>.</span></span></span></span><span><span><span><span>geotools</span></span></span></span><span><span><span><span>.</span></span></span></span>referencing<span><span><span><span>.</span></span></span></span>factory<span><span><span><span>.</span></span></span></span><span><span><span><span>epsg</span></span></span></span><span><span><span><span>.</span></span></span></span>ThreadedHsqlEpsgFactory
 to a 1800000ms timeout</font></div>
<div><font size="1" face="courier new, monospace">May 20, 2014 2:15:10 PM org<span><span><span><span>.</span></span></span></span><span><span><span><span>geotools</span></span></span></span><span><span><span><span>.</span></span></span></span>referencing<span><span><span><span>.</span></span></span></span>factory<span><span><span><span>.</span></span></span></span><span><span><span><span>epsg</span></span></span></span><span><span><span><span>.</span></span></span></span>ThreadedHsqlEpsgFactory
<span><span><span><span>createDataSource</span></span></span></span></font></div>
<div><font size="1" face="courier new, monospace">INFO: Building new data source for org<span><span><span><span>.</span></span></span></span><span><span><span><span>geotools</span></span></span></span><span><span><span><span>.</span></span></span></span>referencing<span><span><span><span>.</span></span></span></span>factory<span><span><span><span>.</span></span></span></span><span><span><span><span>epsg</span></span></span></span><span><span><span><span>.</span></span></span></span>ThreadedHsqlEpsgFactory</font></div>

<div><font size="1" face="courier new, monospace">May 20, 2014 2:15:10 PM org<span><span><span><span>.</span></span></span></span><span><span><span><span>geotools</span></span></span></span><span><span><span><span>.</span></span></span></span>referencing<span><span><span><span>.</span></span></span></span>factory<span><span><span><span>.</span></span></span></span><span><span><span><span>epsg</span></span></span></span><span><span><span><span>.</span></span></span></span>ThreadedHsqlEpsgFactory
<span><span><span><span>createBackingStore</span></span></span></span></font></div>
<div><font size="1" face="courier new, monospace">INFO: Building backing store for org<span><span><span><span>.</span></span></span></span><span><span><span><span>geotools</span></span></span></span><span><span><span><span>.</span></span></span></span>referencing<span><span><span><span>.</span></span></span></span>factory<span><span><span><span>.</span></span></span></span><span><span><span><span>epsg</span></span></span></span><span><span><span><span>.</span></span></span></span>ThreadedHsqlEpsgFactory</font></div>

<div><font size="1" face="courier new, monospace">2014-05-20 14:15:32,105 INFO<span><span><span><span> :</span></span></span></span> [Consumer] - Killing (Actor<span><span><span><span>.</span></span></span></span>act) thread: 0</font></div>

<div><font size="1" face="courier new, monospace">Indexing live with URL: null, and
<span><span><span>params</span></span></span>: null&amp;dataResource=dr0</font></div>
<div><font size="1" face="courier new, monospace"><span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>NullPointerException</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span>at</span></span> au.org.ala.util.CMD$.au$org$ala$util$CMD$$indexDataResourceLive$1(CommandLineTool.scala:371)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span>at</span></span> au.org.ala.util.CMD$$anonfun$executeCommand$2.apply(CommandLineTool.scala:90)</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span>at</span></span> au.org.ala.util.CMD$$anonfun$executeCommand$2.apply(CommandLineTool.scala:86)</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span>
<span><span><span>scala</span></span></span><span><span><span>.</span></span></span>collection<span><span><span>.</span></span></span>IndexedSeqOptimized$class<span><span><span>.</span></span></span><span><span><span>foreach</span></span></span><span><span><span>(</span></span></span>IndexedSeqOptimized<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>33)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span>
<span><span><span>scala</span></span></span><span><span><span>.</span></span></span>collection<span><span><span>.</span></span></span>mutable<span><span><span>.</span></span></span>ArrayOps$ofRef<span><span><span>.</span></span></span><span><span><span>foreach</span></span></span><span><span><span>(</span></span></span>ArrayOps<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>105)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span> au.org.ala.util.CMD$.executeCommand(CommandLineTool.scala:86)</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span> au.org.ala.util.CommandLineTool$.main(CommandLineTool.scala:26)</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span>at</span></span> au.org.ala.util.CommandLineTool.main(CommandLineTool.scala)</font></div>
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<div>Nowadays we use the<b> <span><span>biocache</span></span>-1.0-SNAPSHOT</b> in our environment. But in your last mail you mentioned the version
<b></b><b><span><span>biocache</span></span>-1.1-assembly</b>.<br>
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<div>I did download of this newer <span><span><span>version, but</span></span></span> when I ran it (<font face="courier new, monospace">ingest dr0</font>) in our environment the system showed many errors (see below).</div>

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<div><br>
</div>
<div><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small">log4j:WARN custom level class [org</span><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small"><span>.</span></span><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small"><span>ala</span></span><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small"><span>.</span></span><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small">client</span><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small"><span>.</span></span><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small"><span>appender</span></span><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small"><span>.</span></span><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small">RestL</span><span style="font-family:&#39;courier new&#39;,monospace;font-size:x-small">evel]
 not found.</span><br>
</div>
</div>
<div>
<div><font size="1" face="courier new, monospace">Exception in thread &quot;main&quot; <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>ExceptionInInitializerError</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span> au.org.ala.biocache.load.DataLoader$class.$init$(DataLoader.scala:28)</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span> au.org.ala.biocache.load.Loader.&lt;<span><span><span>init</span></span></span>&gt;(Loader<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>34)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span> au.org.ala.biocache.cmd.CMD$.executeCommand(CMD.scala:29)</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span> au.org.ala.biocache.cmd.CommandLineTool$.main(CommandLineTool.scala:22)</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span> au.org.ala.biocache.cmd.CommandLineTool.main(CommandLineTool.scala)</font></div>
<div><font size="1" face="courier new, monospace">Caused by: <span><span><span>com</span></span></span><span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>CreationException: Guice
 creation errors:</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">1) No implementation for <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>Integer annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span><span><span><span>inject</span></span></span><span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>max<span><span><span>.</span></span></span>connections)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>Integer annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>max<span><span><span>.</span></span></span>connections)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 4 at au.org.ala.biocache.persistence.CassandraPersistenceManager.&lt;<span><span><span>init</span></span></span>&gt;(CassandraPersistenceManager<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>24)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:184)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">2) No implementation for <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>Integer annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span><span><span><span>inject</span></span></span><span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>max<span><span><span>.</span></span></span>retries)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>Integer annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>max<span><span><span>.</span></span></span>retries)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 5 at au.org.ala.biocache.persistence.CassandraPersistenceManager.&lt;<span><span><span>init</span></span></span>&gt;(CassandraPersistenceManager<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>24)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:184)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">3) No implementation for <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>Integer annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span><span><span><span>inject</span></span></span><span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>port)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>Integer annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>port)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 1 at au.org.ala.biocache.persistence.CassandraPersistenceManager.&lt;<span><span><span>init</span></span></span>&gt;(CassandraPersistenceManager<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>24)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:184)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">4) No implementation for <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>Integer annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span><span><span><span>inject</span></span></span><span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=thrift<span><span><span>.</span></span></span>operation<span><span><span>.</span></span></span>timeout)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>Integer annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=thrift<span><span><span>.</span></span></span>operation<span><span><span>.</span></span></span>timeout)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 6 at au.org.ala.biocache.persistence.CassandraPersistenceManager.&lt;<span><span><span>init</span></span></span>&gt;(CassandraPersistenceManager<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>24)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:184)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">5) No implementation for <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span><span><span><span>inject</span></span></span><span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>hosts)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>hosts)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 0 at au.org.ala.biocache.persistence.CassandraPersistenceManager.&lt;<span><span><span>init</span></span></span>&gt;(CassandraPersistenceManager<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>24)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:184)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">6) No implementation for <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span><span><span><span>inject</span></span></span><span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span><span><span><span>keyspace</span></span></span>)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span><span><span><span>keyspace</span></span></span>)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 3 at au.org.ala.biocache.persistence.CassandraPersistenceManager.&lt;<span><span><span>init</span></span></span>&gt;(CassandraPersistenceManager<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>24)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:184)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">7) No implementation for <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span><span><span><span>inject</span></span></span><span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>pool)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=cassandra<span><span><span>.</span></span></span>pool)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 2 at au.org.ala.biocache.persistence.CassandraPersistenceManager.&lt;<span><span><span>init</span></span></span>&gt;(CassandraPersistenceManager<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>24)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:184)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">8) No implementation for <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span><span><span><span>inject</span></span></span><span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=exclude<span><span><span>.</span></span></span>sensitive<span><span><span>.</span></span></span>values)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=exclude<span><span><span>.</span></span></span>sensitive<span><span><span>.</span></span></span>values)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 1 at au.org.ala.biocache.index.SolrIndexDAO.&lt;<span><span><span>init</span></span></span>&gt;(SolrIndexDAO<span><span><span>.</span></span></span><span><span><span>scala</span></span></span><span><span><span>:</span></span></span>28)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:164)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">9) No implementation for <span>
<span>java</span></span><span><span>.</span></span><span><span>lang</span></span><span><span>.</span></span>String annotated with @com<span><span>.</span></span>google<span><span>.</span></span><span><span>inject</span></span><span><span>.</span></span>name<span><span>.</span></span>Named<span><span>(</span></span>value=extra<span><span>.</span></span><span><span>misc</span></span><span><span>.</span></span>fields)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=extra<span><span><span>.</span></span></span><span><span><span>misc</span></span></span><span><span><span>.</span></span></span>fields)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 2 at au.org.ala.biocache.index.SolrIndexDAO.&lt;<span><span>init</span></span>&gt;(SolrIndexDAO<span><span>.</span></span><span><span>scala</span></span><span><span>:</span></span>28)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:164)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">10) No implementation for <span>
<span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span><span><span><span>inject</span></span></span><span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=solr<span><span><span>.</span></span></span>home)
 was bound.</font></div>
<div><font size="1" face="courier new, monospace">  <span><span><span>while</span></span></span> locating
<span><span><span>java</span></span></span><span><span><span>.</span></span></span><span><span><span>lang</span></span></span><span><span><span>.</span></span></span>String annotated with @com<span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>name<span><span><span>.</span></span></span>Named<span><span><span>(</span></span></span>value=solr<span><span><span>.</span></span></span>home)</font></div>

<div><font size="1" face="courier new, monospace">    <span><span><span>for</span></span></span> parameter 0 at au.org.ala.biocache.index.SolrIndexDAO.&lt;<span><span>init</span></span>&gt;(SolrIndexDAO<span><span>.</span></span><span><span>scala</span></span><span><span>:</span></span>28)</font></div>

<div><font size="1" face="courier new, monospace">  <span><span><span>at</span></span></span> au.org.ala.biocache.ConfigModule.configure(Config.scala:164)</font></div>
<div><font size="1" face="courier new, monospace"><br>
</font></div>
<div><font size="1" face="courier new, monospace">10 errors</font></div>
<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span>
<span><span><span>com</span></span></span><span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>internal<span><span><span>.</span></span></span>Errors<span><span><span>.</span></span></span><span><span><span>throwCreationExceptionIfErrorsExist</span></span></span><span><span><span>(</span></span></span>Errors.java<span><span><span>:</span></span></span>354)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span>
<span><span><span>com</span></span></span><span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>InjectorBuilder<span><span><span>.</span></span></span><span><span><span>initializeStatically</span></span></span><span><span><span>(</span></span></span>InjectorBuilder.java<span><span><span>:</span></span></span>152)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span>
<span><span><span>com</span></span></span><span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>InjectorBuilder<span><span><span>.</span></span></span>build<span><span><span>(</span></span></span>InjectorBuilder.java<span><span><span>:</span></span></span>105)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span>
<span><span><span>com</span></span></span><span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>Guice<span><span><span>.</span></span></span><span><span><span>createInjector</span></span></span><span><span><span>(</span></span></span>Guice.java<span><span><span>:</span></span></span>92)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span>
<span><span><span>com</span></span></span><span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>Guice<span><span><span>.</span></span></span><span><span><span>createInjector</span></span></span><span><span><span>(</span></span></span>Guice.java<span><span><span>:</span></span></span>69)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span>
<span><span><span>com</span></span></span><span><span><span>.</span></span></span>google<span><span><span>.</span></span></span>inject<span><span><span>.</span></span></span>Guice<span><span><span>.</span></span></span><span><span><span>createInjector</span></span></span><span><span><span>(</span></span></span>Guice.java<span><span><span>:</span></span></span>59)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span> au.org.ala.biocache.Config$.&lt;<span><span>init</span></span>&gt;(Config<span><span>.</span></span><span><span>scala</span></span><span><span>:</span></span>24)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span><span><span><span>at</span></span></span> au.org.ala.biocache.Config$.&lt;<span><span><span>clinit</span></span></span>&gt;(Config<span><span><span>.</span></span></span><span><span><span>scala</span></span></span>)</font></div>

<div><font size="1" face="courier new, monospace"><span style="white-space:pre-wrap"></span>... 5 more</font></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>Related to these specific issues (data update and incremental load), I will need to upgrade the <span>biocache</span> 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?<br>
</div>
</div>
<div class="gmail_extra"><br>
Which layer files should I include in my environment to run these tests?</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Thanks!</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Regards,</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">
<div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px">
<div class="gmail_extra" style="color:rgb(136,136,136)">Daniel Lins da Silva</div>
<div class="gmail_extra" style="color:rgb(136,136,136)">(Mobile) <a href="tel:55%2011%2096144-4050" value="+5511961444050" target="_blank">55 11 96144-4050</a></div>
<div style="color:rgb(136,136,136)">
<div class="gmail_extra"><font color="#000000">Research Center <span>on</span> Biodiversity and Computing (Biocomp)</font></div>
<div class="gmail_extra"><font color="#000000">University of Sao Paulo, Brazil</font></div>
</div>
<div class="gmail_extra" style="color:rgb(136,136,136)"><a href="mailto:daniellins@usp.br" target="_blank">daniellins@usp.br</a></div>
<div class="gmail_extra" style="color:rgb(136,136,136)"><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a></div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">2014-05-09 2:14 GMT-03:00 <span dir="ltr">&lt;<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr">&gt;</span><span>:</span><span></span><span></span><span></span><span></span><span></span><span></span><span></span><span></span><span></span><br>

<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:rgb(0,0,0);font-size:10pt">
Thanks Daniel. 
<div><br>
</div>
<div>I&#39;ve spotted the problem:</div>
<div>
<div><br>
</div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span>java</span></span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"> -</span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span>cp</span></span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span> .</span></span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span>:</span></span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span>biocache</span></span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span>.</span></span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px">jar
 au.org.ala.util.DwcCSVLoader dr0 -l dataset-updated</span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span>.</span></span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span>csv</span></span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"> -</span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span>b</span></span><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"> true</span></div>

<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><br>
</span></div>
</div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><span>this</span> bypasses lookups against the
<span>collectory</span> for the metadata. </span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><br>
</span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px">To load this dataset, you can use the
<span>biocache</span> <span>commandline</span> tool like so:</span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><br>
</span></div>
<div>
<p></p>
<p>$ <span>java</span> -<span>cp</span> /usr/lib/<span>biocache</span><span>:</span>/usr/lib/<span>biocache</span>/<span>biocache</span>-store-1.1-assembly<span>.</span>jar -Xms2g -Xmx2g au.org.ala.biocache.cmd.CommandLineTool</p>

<p><br>
</p>
<p>----------------------------</p>
<p>| <span>Biocache</span> management tool |</p>
<p>----------------------------</p>
<p><span style="font-size:10pt">Please supply a command or hit ENTER to view command list.</span><span style="font-size:10pt"> </span></p>
<p><span>biocache</span>&gt; ingest dr8</p>
</div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><br>
</span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px">This will:</span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><br>
</span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px">1) Retrieve the metadata from the configured instance of the
<span>collectory</span></span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px">2) Load, process, sample (if there are layers configured and available) and index</span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><br>
</span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px">Cheers</span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px"><br>
</span></div>
<div><span style="font-family:&#39;Times New Roman&#39;;font-size:16px">Dave</span></div>
<div><br>
</div>
<div>
<div>
<div style="font-family:&#39;Times New Roman&#39;;color:rgb(0,0,0);font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> Daniel Lins [<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>]<br>
<b>Sent:</b> 09 May 2014 14:27
<div>
<div><br>
<b>To:</b> Martin, Dave (CES, Black Mountain)<br>
<b>Cc:</b> <a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a>; dos Remedios, Nick (CES, Black Mountain); Pedro Corrêa; Nicholls, Miles (CES, Black Mountain)<br>
<b>Subject:</b> Re: [Ala-portal] DwC-A loading <span>problems</span><br>
</div>
</div>
</font><br>
</div>
<div>
<div>
<div></div>
<div>
<div dir="ltr">David,
<div><br>
</div>
<div>The dr0 configuration:</div>
<div><br>
</div>
<div><a href="https://www.dropbox.com/s/lsy11jadwmyghjj/collectoryConfig1.png" target="_blank">https://www.dropbox.com/s/lsy11jadwmyghjj/collectoryConfig1.png</a><br>
</div>
<div><br>
</div>
<div>Sorry, but this server doesn&#39;t have external access yet.</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2014-05-09 1:06 GMT-03:00 <span dir="ltr">&lt;<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr">&gt;</span><span>:</span><br>

<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:rgb(0,0,0);font-size:10pt">
As an example of what it should look like, see:<br>
<br>
<a href="http://ala-demo.gbif.org/collectory/dataResource/edit/dr8?page=contribution" target="_blank">http://ala-demo.gbif.org/collectory/dataResource/edit/dr8?page=contribution</a><br>
<div><br>
</div>
<div><br>
<div>
<div style="font-family:&#39;Times New Roman&#39;;color:rgb(0,0,0);font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> Daniel Lins [<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>]
<div><br>
<b>Sent:</b> 09 May 2014 13:59<br>
<b>To:</b> Martin, Dave (CES, Black Mountain)<br>
<b>Cc:</b> <a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a>; dos Remedios, Nick (CES, Black Mountain); Pedro Corrêa; Nicholls, Miles (CES, Black Mountain)<br>
</div>
<div>
<div><b>Subject:</b> Re: [Ala-portal] DwC-A loading <span>problems</span><br>
</div>
</div>
</font><br>
</div>
<div>
<div>
<div></div>
<div>
<div dir="ltr">Thanks David,
<div><br>
</div>
<div>We use the DwC term &quot;<span><span>occurrenceID</span></span>&quot; to identify the records. It&#39;s a unique key.</div>
<div><br>
</div>
<div>
<div>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). <br>
</div>
</div>
<div><br>
</div>
<div>For instance (update of locality).</div>
<div><br>
</div>
<div>Load 1 ($ <span><span><span>java</span></span></span> -<span><span><span>cp</span></span></span><span><span><span> .</span></span></span><span><span><span>:</span></span></span><span><span><span>biocache</span></span></span><span><span><span>.</span></span></span>jar
 au.org.ala.util.DwcCSVLoader dr0 -l dataset.csv -<span><span><span>b</span></span></span> true)</div>
<div><br>
</div>
<div><font color="#38761d">{<span><span><span>OccurrenceID</span></span></span>: 1, municipality: Sao Paulo,<span><span><span> ...</span></span></span>},</font></div>
<div><font color="#3d85c6">{<span><span><span>OccurrenceID</span></span></span>: 2, municipality: Sao Paulo,<span><span><span> ...</span></span></span>}</font></div>
<div><br>
</div>
<div>Process 1 (biocache$ process dr0)</div>
<div>Index 1 (biocache$ index dr0)</div>
<div><br>
</div>
<div>Load 2 (updated records and new records) (($ <span><span><span>java</span></span></span> -<span><span><span>cp</span></span></span><span><span><span> .</span></span></span><span><span><span>:</span></span></span><span><span><span>biocache</span></span></span><span><span><span>.</span></span></span>jar
 au.org.ala.util.DwcCSVLoader dr0 -l dataset-updated<span><span><span>.</span></span></span><span><span><span>csv</span></span></span> -<span><span><span>b</span></span></span> true)</div>
<div>
<div><br>
</div>
<div><font color="#38761d">{<span><span><span>OccurrenceID</span></span></span>: 1, </font><span style="color:rgb(56,118,29)">municipality</span><font color="#38761d">: Rio
<span>de</span> Janeiro,<span><span><span> ...</span></span></span>},</font></div>
<div><font color="#3d85c6">{<span><span><span>OccurrenceID</span></span></span>: 2, </font><span style="color:rgb(61,133,198)">municipality</span><font color="#3d85c6">: Rio
<span>de</span> Janeiro,<span><span><span> ...</span></span></span>},</font></div>
</div>
<div>{<span><span><span>OccurrenceID</span></span></span>: 3, municipality: Sao Paulo,<span><span><span> ...</span></span></span>}<br>
</div>
<div><br>
</div>
<div>
<div>Process 2 (biocache$ process dr0)</div>
<div>Index 2 (biocache$ index dr0)</div>
</div>
<div><br>
</div>
<div>Results shown by ALA:</div>
<div><br>
</div>
<div>
<div><font color="#38761d">{<span><span><span>OccurrenceID</span></span></span>: 1, </font><span style="color:rgb(56,118,29)">municipality</span><font color="#38761d">: </font><span style="color:rgb(56,118,29)">Sao Paulo</span><font color="#38761d">,<span><span><span> ...</span></span></span>},</font></div>

<div><font color="#3d85c6">{<span><span>OccurrenceID</span></span>: 2, </font><span style="color:rgb(61,133,198)">municipality</span><font color="#3d85c6">: </font><span style="color:rgb(61,133,198)">Sao Paulo</span><font color="#3d85c6">,<span><span> ...</span></span>},</font></div>

</div>
<div>
<div>
<div><font color="#38761d">{<span><span>OccurrenceID</span></span>: 1, </font><span style="color:rgb(56,118,29)">municipality</span><font color="#38761d">: </font><span style="color:rgb(56,118,29)">Rio
<span>de</span> Janeiro</span><font color="#38761d">,<span><span> ...</span></span>},</font></div>
<div><font color="#3d85c6">{<span><span>OccurrenceID</span></span>: 2, </font><span style="color:rgb(61,133,198)">municipality</span><font color="#3d85c6">: </font><span style="color:rgb(61,133,198)">Rio
<span>de</span> Janeiro</span><font color="#3d85c6">,<span><span> ...</span></span>}</font></div>
</div>
</div>
<div>{<span><span><span>OccurrenceID</span></span></span>: 3, municipality: Sao Paulo,<span><span><span> ...</span></span></span>}<br>
</div>
<div><br>
</div>
<div>But I expected:</div>
<div><br>
</div>
<div>
<div><span style="color:rgb(56,118,29)">{<span><span>OccurrenceID</span></span>: 1, </span><span style="color:rgb(56,118,29)">municipality</span><span style="color:rgb(56,118,29)">: </span><span style="color:rgb(56,118,29)">Rio
<span>de</span> Janeiro</span><span style="color:rgb(56,118,29)">,<span><span> ...</span></span>},</span><br>
</div>
<div>
<div><font color="#3d85c6">{<span><span>OccurrenceID</span></span>: 2, </font><span style="color:rgb(61,133,198)">municipality</span><font color="#3d85c6">: </font><span style="color:rgb(61,133,198)">Rio
<span>de</span> Janeiro</span><font color="#3d85c6">,<span><span> ...</span></span>}</font></div>
</div>
<div>{<span><span><span>OccurrenceID</span></span></span>: 3, municipality: Sao Paulo,<span><span><span> ...</span></span></span>}</div>
</div>
<div><br>
</div>
<div>I need to delete (delete-resource function) existing data before the reload? If no, what I did wrong to generate this data duplication?</div>
<div><br>
</div>
<div>Thanks! </div>
<div><br>
</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
Daniel Lins da Silva</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
(Mobile) <a href="tel:55%2011%2096144-4050" value="+5511961444050" target="_blank">55 11 96144-4050</a></div>
<div style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<div class="gmail_extra"><font color="#000000">Research Center <span><span><span>on</span></span></span> Biodiversity and Computing (Biocomp)</font></div>
<div class="gmail_extra"><font color="#000000">University of Sao Paulo, Brazil</font></div>
</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<a href="mailto:daniellins@usp.br" target="_blank">daniellins@usp.br</a></div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div> </div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2014-05-07 0:46 GMT-03:00 <span dir="ltr">&lt;<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a></span><span dir="ltr"></span><span dir="ltr">&gt;</span><span>:</span><br>

<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:rgb(0,0,0);font-size:10pt">
<div>
<div>Thanks Daniel. Natasha has now left the ALA.</div>
<div><br>
</div>
<div>The uniqueness of records is determined by <span>information</span> stored in the
<span>collectory</span>. See screenshot [1].</div>
<div><span style="font-size:10pt">By default, &quot;<span>catalogNumber</span>&quot; is <span>
used but</span> you can change this to any number of fields that should be stable in the data. </span></div>
<div>Using unstable fields for the ID isn&#39;t recommended (e.g. <span>scientificName</span>).  To update the records, the process is to just re-load the dataset.</div>
<div><br>
</div>
<div>Automatically loaded - this <span>isnt</span> in use and we may remove from the UI in future iterations.</div>
<div>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.</div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
</div>
<div>Dave Martin</div>
</div>
<div>ALA</div>
<div><br>
</div>
<div>[1] <a href="http://bit.ly/1g72HFN" style="font-size:10pt" target="_blank">http://bit.ly/1g72HFN</a></div>
<div><br>
</div>
<div style="font-family:&#39;Times New Roman&#39;;color:rgb(0,0,0);font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> Daniel Lins [<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>]<br>
<b>Sent:</b> 05 May 2014 15:39<br>
<b>To:</b> Quimby, Natasha (CES, Black Mountain)<br>
<b>Cc:</b> <a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a>; dos Remedios, Nick (CES, Black Mountain); Martin, Dave (CES, Black Mountain); Pedro Corrêa<br>
<b>Subject:</b> Re: [Ala-portal] DwC-A loading <span><span>problems</span></span><br>
</font><br>
</div>
<div>
<div>
<div></div>
<div>
<div dir="ltr">
<div>
<div>Hi Natasha, </div>
<div><br>
</div>
<div>I managed to import the DwC-A file following the steps reported in the previous email. Thank you!</div>
<div><br>
</div>
<div>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
<span><span>occurrenceID</span></span> (I did set in the data resource configuration to use &quot;OcurrenceID&quot; to uniquely identify a record).</div>
<div><br>
</div>
<div>How can I update existing records in the database? For instance, the location&#39;s metadata of an occurrence record stored in my database?</div>
<div><br>
</div>
<div>I also would like to better understand the behavior of the properties &quot;Automatically loaded&quot; and &quot;Incremental Load&quot;. </div>
</div>
<div><br>
</div>
<div>Thanks!!</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
Daniel Lins da Silva</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
(Mobile) <a href="tel:55%2011%2096144-4050" value="+5511961444050" target="_blank">55 11 96144-4050</a></div>
<div style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<div class="gmail_extra"><font color="#000000">Research Center <span><span><span>on</span></span></span> Biodiversity and Computing (Biocomp)</font></div>
<div class="gmail_extra"><font color="#000000">University of Sao Paulo, Brazil</font></div>
</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<a href="mailto:daniellins@usp.br" target="_blank">daniellins@usp.br</a></div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px;color:rgb(136,136,136)">
<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2014-04-28 3:52 GMT-03:00 Daniel Lins <span dir="ltr">&lt;<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>&gt;</span>:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">Thanks Natasha!
<div><br>
</div>
<div>I will try your recommendations. Once finished, I will contact you.</div>
<div><br>
</div>
<div>Regards<br>
</div>
<div class="gmail_extra">
<div><br>
<div class="gmail_extra" style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">
Daniel Lins da Silva</div>
<div class="gmail_extra" style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">
(Mobile) <a href="tel:55%2011%2096144-4050" value="+5511961444050" target="_blank">55 11 96144-4050</a></div>
<div style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">
<div class="gmail_extra"><font color="#000000">Research Center <span><span><span><span>on</span></span></span></span> Biodiversity and Computing (Biocomp)</font></div>
<div class="gmail_extra"><font color="#000000">University of Sao Paulo, Brazil</font></div>
</div>
<div class="gmail_extra" style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">
<a href="mailto:daniellins@usp.br" target="_blank">daniellins@usp.br</a></div>
<div class="gmail_extra" style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">
<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a></div>
<div class="gmail_extra" style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">
<br>
</div>
<div class="gmail_extra" style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">
<br>
</div>
<br>
</div>
<div class="gmail_quote">2014-04-28 3:26 GMT-03:00 <span dir="ltr">&lt;<a href="mailto:Natasha.Quimby@csiro.au" target="_blank">Natasha.Quimby@csiro.au</a></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr"></span><span dir="ltr">&gt;</span><span>:</span><span></span><span></span><span></span><span></span>
<div>
<div><br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Hi Daniel,</div>
<div><br>
</div>
<div>When you specify a local DwcA Load the archive needs to be unzipped. Try unzipping <b>2f676abc-4503-489e-8f0c-fcb6e1bc554b<span><span><span>.</span></span></span>zip
</b>and then running the following:</div>
<div>
<div><span><span><span>s<b>udo</b></span><b></b></span><b></b><b></b><b></b></span><b>
<span><span><span>java</span></span></span> -<span><span><span>cp</span></span></span><span><span><span> .</span></span></span>:biocache.jar au.org.ala.util.DwCALoader dr7 -l /data/collectory/upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b</b></div>

<div><b><br>
</b></div>
</div>
<div>If you configure the <span><span><span>collectory</span></span></span> to provide the
<span><span><span>dwca</span></span></span> the <span><span><span>biocache</span></span></span> automatically unzips the archive for you.  You would need to configure dr7 with the following connection parameters:</div>
<div><br>
</div>
<div>&quot;<span><span><span>protocol</span></span></span>&quot;:&quot;DwCA&quot;</div>
<div>&quot;<span><span><span>termsForUniqueKey</span></span></span>&quot;<span><span><span>:</span></span></span>[&quot;<span><span><span>occurrenceID</span></span></span>&quot;],</div>
<div><span>&quot;url&quot;:&quot;file:////data/collectory/upload/</span>1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b.zip<span>&quot;</span></div>
<div><b><br>
</b></div>
<div>You could then load the resource by:</div>
<div>
<div><span><span><span>s<b>udo</b></span><b></b></span><b></b><b></b><b></b></span><b>
<span><span><span>java</span></span></span> -<span><span><span>cp</span></span></span><span><span><span> .</span></span></span><span><span><span>:</span></span></span><span><span><span>biocache</span></span></span><span><span><span>.</span></span></span>jar
 au.org.ala.util.DwCALoader dr7</b></div>
<div><b><br>
</b></div>
</div>
<div>If you continue to have <span><span><span><span>issues please</span></span></span></span> let us know. </div>
<div><br>
</div>
<div>Hope that this helps.</div>
<div><br>
</div>
<div>Regards</div>
<div>Natasha</div>
<div><br>
</div>
<span>
<div style="border-width:1pt medium medium;border-style:solid none none;padding:3pt 0in 0in;text-align:left;font-size:11pt;font-family:Calibri;border-top-color:rgb(181,196,223)">
<span style="font-weight:bold">From: </span>Daniel Lins &lt;<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>&gt;<br>
<span style="font-weight:bold">Date: </span>Monday, 28 April 2014 3:54 PM<br>
<span style="font-weight:bold">To: </span><span><span><span><span>&quot;<a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a>&quot; &lt;<a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a></span><a href="mailto:ala-portal@lists.gbif.org" target="_blank"></a></span><a href="mailto:ala-portal@lists.gbif.org" target="_blank"></a></span><a href="mailto:ala-portal@lists.gbif.org" target="_blank"></a><a href="mailto:ala-portal@lists.gbif.org" target="_blank"></a><a href="mailto:ala-portal@lists.gbif.org" target="_blank"></a></span><a href="mailto:ala-portal@lists.gbif.org" target="_blank"></a><span><span><span><span>&gt;,</span></span></span></span>
 &quot;dos Remedios, Nick (CES, Black Mountain)&quot; &lt;<a href="mailto:Nick.Dosremedios@csiro.au" target="_blank">Nick.Dosremedios@csiro.au</a><span><span><span><span>&gt;,</span></span></span></span> &quot;Martin, Dave (CES, Black Mountain)&quot; &lt;<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a>&gt;<br>

<span style="font-weight:bold">Subject: </span>[Ala-portal] DwC-A loading <span><span><span><span>problems</span></span></span></span><br>
</div>
<div>
<div>
<div><br>
</div>
<blockquote style="border-left:#b5c4df 5 solid;padding:0 0 0 5;margin:0 0 0 5">
<div>
<div>
<div dir="ltr">Hi Nick and Dave,
<div><br>
</div>
<div>We are having some problems in Biocache during the upload of DwC-A files.</div>
<div><br>
</div>
<div>
<div>As shown below, after run the method &quot;au.org.ala.util.DwCALoader&quot;, our system returns the error message
<font color="#ff0000">&quot;Exception in thread &quot;main&quot; org<span><span><span><span>.</span></span></span></span><span><span><span><span>gbif</span></span></span></span><span><span><span><span>.</span></span></span></span><span><span><span><span>dwc</span></span></span></span><span><span><span><span>.</span></span></span></span>text<span><span><span><span>.</span></span></span></span>UnkownDelimitersException:
 Unable to detect field delimiter&quot;</font></div>
<div><br>
</div>
<div>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.</div>
</div>
<div><br>
</div>
<div>What causes these problems? (** CSV Loader works great)<br>
</div>
<div><br>
</div>
<div><b><i><span><span><span><span><span>tab</span></span></span></span></span>-delimited file test</i></b></div>
<div><b><br>
</b></div>
<div>
<div>poliusp@poliusp-VirtualBox:~/dev/biocache$ s<b>udo java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7 -l /data/collectory/upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b.zip</b></div>
<div>2014-04-28 01:44:02,837 INFO<span><span><span><span><span> :</span></span></span></span></span> [<span><span><span><span><span>ConfigModule</span></span></span></span></span>] - Loading configuration from /data/biocache/config/biocache-config.properties</div>

<div>2014-04-28 01:44:03,090 INFO<span><span><span><span><span> :</span></span></span></span></span> [<span><span><span><span><span>ConfigModule</span></span></span></span></span>] - Initialise SOLR</div>
<div>2014-04-28 01:44:03,103 INFO<span><span><span><span><span> :</span></span></span></span></span> [<span><span><span><span><span>ConfigModule</span></span></span></span></span>] -
<span><span><span><span><span>Initialise</span></span></span></span></span> name matching indexes</div>
<div>2014-04-28 01:44:03,605 INFO<span><span><span><span><span> :</span></span></span></span></span> [<span><span><span><span><span>ConfigModule</span></span></span></span></span>] - Initialise persistence manager</div>
<div>2014-04-28 01:44:03,606 INFO<span><span><span><span><span> :</span></span></span></span></span> [<span><span><span><span><span>ConfigModule</span></span></span></span></span>] - Configure complete</div>
<div>Loading archive /data/<span><span><span><span><span>collectory</span></span></span></span></span>/upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b<span><span><span><span><span>.</span></span></span></span></span>zip for resource dr7 with unique
 terms List<span><span><span><span><span>(</span></span></span></span></span><span><span><span><span><span>dwc</span></span></span></span></span><span><span><span><span><span>:</span></span></span></span></span><span><span><span><span><span>occurrenceID</span></span></span></span></span>)
 stripping spaces false incremental false testing <span><span><span><span><span>false</span></span></span></span></span></div>
<div><b>Exception in thread &quot;main&quot; org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>gbif</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>dwc</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>text<span><span><span><span><span>.</span></span></span></span></span>UnkownDelimitersException:
 Unable to detect field delimiter</b></div>
<div>        <span><span><span><span><span>at</span></span></span></span></span> org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>gbif</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>file<span><span><span><span><span>.</span></span></span></span></span>CSVReaderFactory<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>buildArchiveFile</span></span></span></span></span><span><span><span><span><span>(</span></span></span></span></span>CSVReaderFactory.java<span><span><span><span><span>:</span></span></span></span></span>129)</div>

<div>        <span><span><span><span><span>at</span></span></span></span></span> org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>gbif</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>file<span><span><span><span><span>.</span></span></span></span></span>CSVReaderFactory<span><span><span><span><span>.</span></span></span></span></span>build<span><span><span><span><span>(</span></span></span></span></span>CSVReaderFactory.java<span><span><span><span><span>:</span></span></span></span></span>46)</div>

<div>        <span><span><span><span><span>at</span></span></span></span></span> org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>gbif</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>dwc</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>text<span><span><span><span><span>.</span></span></span></span></span>ArchiveFactory<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>readFileHeaders</span></span></span></span></span><span><span><span><span><span>(</span></span></span></span></span>ArchiveFactory.java<span><span><span><span><span>:</span></span></span></span></span>344)</div>

<div>        <span><span><span><span><span>at</span></span></span></span></span> org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>gbif</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>dwc</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>text<span><span><span><span><span>.</span></span></span></span></span>ArchiveFactory<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>openArchive</span></span></span></span></span><span><span><span><span><span>(</span></span></span></span></span>ArchiveFactory.java<span><span><span><span><span>:</span></span></span></span></span>289)</div>

<div>        <span><span><span><span><span>at</span></span></span></span></span> au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129)</div>
<div>        <span><span><span><span><span>at</span></span></span></span></span> au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106)</div>
<div>        <span><span><span><span>at</span></span></span></span> au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52)</div>
<div>        <span><span><span><span>at</span></span></span></span> au.org.ala.util.DwCALoader.main(DwCALoader.scala)</div>
<div><br>
</div>
<div><br>
</div>
<div><b><i><span><span><span><span>comma</span></span></span></span>-delimited file test</i></b><br>
</div>
<div><br>
</div>
<div>
<div>poliusp@poliusp-VirtualBox:~/dev/biocache$ <b>sudo java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7 -l ./<span><span><span><span>dwca</span></span></span></span>-teste3<span><span><span><span>.</span></span></span></span>zip</b></div>

<div>2014-04-28 01:56:04,683 INFO<span><span><span><span> :</span></span></span></span> [<span><span><span><span>ConfigModule</span></span></span></span>] - Loading configuration from /data/biocache/config/biocache-config.properties</div>

<div>2014-04-28 01:56:04,940 INFO<span><span><span><span> :</span></span></span></span> [<span><span><span><span>ConfigModule</span></span></span></span>] - Initialise SOLR</div>
<div>2014-04-28 01:56:04,951 INFO<span><span><span><span> :</span></span></span></span> [<span><span><span><span>ConfigModule</span></span></span></span>] -
<span><span><span><span>Initialise</span></span></span></span> name matching indexes</div>
<div>2014-04-28 01:56:05,437 INFO<span><span><span><span> :</span></span></span></span> [<span><span><span><span>ConfigModule</span></span></span></span>] - Initialise persistence manager</div>
<div>2014-04-28 01:56:05,438 INFO<span><span><span><span> :</span></span></span></span> [<span><span><span><span>ConfigModule</span></span></span></span>] - Configure complete</div>
<div>Loading archive<span><span><span><span> .</span></span></span></span>/<span><span><span><span>dwca</span></span></span></span>-teste3<span><span><span><span>.</span></span></span></span>zip for resource dr7 with unique terms List<span><span><span><span>(</span></span></span></span><span><span><span><span>dwc</span></span></span></span><span><span><span><span>:</span></span></span></span><span><span><span><span>occurrenceID</span></span></span></span>)
 stripping spaces false incremental false testing <span><span><span><span>false</span></span></span></span></div>
<div><b>Exception in thread &quot;main&quot; org<span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>gbif</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span><span><span><span><span><span>dwc</span></span></span></span></span><span><span><span><span><span>.</span></span></span></span></span>text<span><span><span><span><span>.</span></span></span></span></span>UnkownDelimitersException:
 Unable to detect field delimiter</b></div>
<div>        <span><span><span><span>at</span></span></span></span> org<span><span><span><span>.</span></span></span></span><span><span><span><span>gbif</span></span></span></span><span><span><span><span>.</span></span></span></span>file<span><span><span><span>.</span></span></span></span>CSVReaderFactory<span><span><span><span>.</span></span></span></span><span><span><span><span>buildArchiveFile</span></span></span></span><span><span><span><span>(</span></span></span></span>CSVReaderFactory.java<span><span><span><span>:</span></span></span></span>129)</div>

<div>        <span><span><span><span>at</span></span></span></span> org<span><span><span><span>.</span></span></span></span><span><span><span><span>gbif</span></span></span></span><span><span><span><span>.</span></span></span></span>file<span><span><span><span>.</span></span></span></span>CSVReaderFactory<span><span><span><span>.</span></span></span></span>build<span><span><span><span>(</span></span></span></span>CSVReaderFactory.java<span><span><span><span>:</span></span></span></span>46)</div>

<div>        <span><span><span><span>at</span></span></span></span> org<span><span><span><span>.</span></span></span></span><span><span><span><span>gbif</span></span></span></span><span><span><span><span>.</span></span></span></span><span><span><span><span>dwc</span></span></span></span><span><span><span><span>.</span></span></span></span>text<span><span><span><span>.</span></span></span></span>ArchiveFactory<span><span><span><span>.</span></span></span></span><span><span><span><span>readFileHeaders</span></span></span></span><span><span><span><span>(</span></span></span></span>ArchiveFactory.java<span><span><span><span>:</span></span></span></span>344)</div>

<div>        <span><span><span><span>at</span></span></span></span> org<span><span><span><span>.</span></span></span></span><span><span><span><span>gbif</span></span></span></span><span><span><span><span>.</span></span></span></span><span><span><span><span>dwc</span></span></span></span><span><span><span><span>.</span></span></span></span>text<span><span><span><span>.</span></span></span></span>ArchiveFactory<span><span><span><span>.</span></span></span></span><span><span><span><span>openArchive</span></span></span></span><span><span><span><span>(</span></span></span></span>ArchiveFactory.java<span><span><span><span>:</span></span></span></span>289)</div>

<div>        <span><span><span><span><span>at</span></span></span></span></span> au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129)</div>
<div>        <span><span><span><span><span>at</span></span></span></span></span> au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106)</div>
<div>        <span><span><span><span><span>at</span></span></span></span></span> au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52)</div>
<div>        <span><span><span><span><span>at</span></span></span></span></span> au.org.ala.util.DwCALoader.main(DwCALoader.scala)</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Thanks!</div>
<div><br>
</div>
<div>Regards.</div>
-- <br>
<div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px">Daniel Lins da Silva</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px">(Mobile) <a href="tel:55%2011%2096144-4050" value="+5511961444050" target="_blank">55 11 96144-4050</a></div>
<div style="font-family:arial,sans-serif;font-size:13px">
<div class="gmail_extra"><font color="#000000">Research Center <span><span><span><span>on</span></span></span></span> Biodiversity and Computing (Biocomp)</font></div>
<div class="gmail_extra"><font color="#000000">University of Sao Paulo, Brazil</font></div>
</div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px"><a href="mailto:daniellins@usp.br" target="_blank">daniellins@usp.br</a></div>
<div class="gmail_extra" style="font-family:arial,sans-serif;font-size:13px"><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a></div>
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<span><font color="#888888"><br>
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-- <br>
<div>Daniel Lins da Silva<br>
(<span><span>Cel</span></span>) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
</div>
</font></span></div>
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-- <br>
<div>Daniel Lins da Silva<br>
(<span><span>Cel</span></span>) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
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</div>
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</blockquote>
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<br>
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<div><br>
</div>
-- <br>
<div>Daniel Lins da Silva<br>
(<span>Cel</span>) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
</div>
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</blockquote>
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<span><font color="#888888">
<div><br>
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-- <br>
<div>Daniel Lins da Silva<br>
(<span>Cel</span>) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
</div>
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<br clear="all">
<div><br>
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-- <br>
<div>Daniel Lins da Silva<br>
(Cel) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
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-- <br>
<div>Daniel Lins da Silva<br>
(Cel) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
</div>
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<span><font color="#888888"><br>
<br clear="all">
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<div><br>
</div>
-- <br>
<div>Daniel Lins da Silva<br>
(Cel) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
</div>
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-- <br>
<div>Daniel Lins da Silva<br>
(Cel) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
</div>
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<br clear="all">
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-- <br>
<div>Daniel Lins da Silva<br>
(Cel) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div>Daniel Lins da Silva<br>(Cel) 11 6144-4050</div><div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br></div>
</div>