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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Thanks Santiago, Burke.
<div><br>
</div>
<div>The recommended approach for all projects is to load data following the instructions that Burke included in his last email [1].</div>
<div>One of the requirements for this to work is that an instance of the collectory is installed.</div>
<div>What Natasha described (and which is now out of date) is a mechanism for loading data without a collectory instance. This is useful for local development purposes only.</div>
<div>This can be done on the command line with version 1.1 with the command:</div>
<div><br>
</div>
<div>biocache>> load-local-csv dr0 /tmp/my-csv.txt</div>
<div><br>
</div>
<div>The way we load data in our production environment is as follows:</div>
<div><br>
</div>
<div>1) Create a data resource in the collectory</div>
<div>2) Upload a CSV or DwC-A zip file into the collectory using the "Upload file" option</div>
<div>3) Use the command line tool describe in [1] to load, sample (optional), process and index the data</div>
<div><br>
</div>
<div>Hope this helps.</div>
<div><br>
</div>
<div>Dave Martin</div>
<div>ALA</div>
<div>[1] <a href="https://code.google.com/p/ala-portal/wiki/LoadBiocacheData" target="_blank" style="font-family: 'Times New Roman', serif; font-size: 16px;">https://code.google.com/p/ala-portal/wiki/LoadBiocacheData</a></div>
<div><br>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF744838" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> ala-portal-bounces@lists.gbif.org [ala-portal-bounces@lists.gbif.org] on behalf of Santiago [sama@gbif.es]<br>
<b>Sent:</b> 29 May 2014 19:08<br>
<b>To:</b> 'Burke Chih-Jen Ko [GBIF]'<br>
<b>Cc:</b> Ala-portal@lists.gbif.org<br>
<b>Subject:</b> Re: [Ala-portal] Installation page updated<br>
</font><br>
</div>
<div></div>
<div>
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Hi Burke,</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">I think that you can use
</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> the
</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">instructions</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> that you refer in your mail</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">
when you are running from inside CSIRO/ALA, please someone correct me if I’m wrong.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">I´m going to tell you my experience:</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">When I want to index a resource I use biocache.jar</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">.
</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">I</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">
</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">use two options: Load a resource via CSV or via Dwc-A. I attach a mail in which Natasha explains how we can load a resource via Dwc-A.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">If I want to load a resource through CSV, I execute the next command:</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt; font-family:"Courier New"">java -cp .:biocache.jar au.org.ala.util.DwcCSVLoader drtest -l path-to-file.csv -b true</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">When you have loaded the resource you have to enter in the biocache command line, then you must execute “ >biocache” and then you can process
and index the loaded resource. “> process drtest” and “>index drtest”.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">My problem is that when I want to load a resource via Dwc-A and I execute:
</span><span lang="EN-US" style="font-size:10.0pt; font-family:"Courier New"">java -cp .:biocache.jar au.org.ala.util.DwCALoader drtest</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">The system doesn’t find the class: </span><span lang="EN-US" style="font-size:10.0pt; font-family:"Courier New"">au.org.ala.util.DwCALoader</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">.
It´s very weird.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Could you check if you can do this? I mean, could you check if you can load a resource in the way Natasha explained in her mail?</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">The mappings. I don’t understand one thing. How is it possible that in the demo-portal
</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"><a href="http://ala-ono.it.csiro.au/generic-hub/occurrences/de34b076-e436-4314-a769-969f8ef36273" target="_blank"><span lang="EN-US">http://ala-ono.it.csiro.au/generic-hub/occurrences/de34b076-e436-4314-a769-969f8ef36273</span></a></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">,
I can see the information in the right way? This is an example of a Spanish resource from GBIF.org. The occurrences are been loaded, processed and indexed. How is that in our installation we must to do something else if in that installation we can see the
indexed occurrences correctly, It is the same installation, right??</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Kind regards.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">SaMa</span><span lang="EN-US" style="font-size:10.0pt; font-family:"Courier New""></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
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<div style="border:none; border-top:solid #B5C4DF 1.0pt; padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:10.0pt; font-family:"Tahoma","sans-serif"">De:</span></b><span style="font-size:10.0pt; font-family:"Tahoma","sans-serif""> Burke Chih-Jen Ko [GBIF] [mailto:bko@gbif.org]
<br>
<b>Enviado el:</b> jueves, 29 de mayo de 2014 9:48<br>
<b>Para:</b> Santiago Martinez de la Riva<br>
<b>CC:</b> Ala-portal@lists.gbif.org<br>
<b>Asunto:</b> Re: [Ala-portal] Installation page updated</span></p>
</div>
</div>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Hi Sama,</p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Yes I did but I use country DwC-A downloaded from GBIF Portal. I basically follow the instruction on <a href="https://code.google.com/p/ala-portal/wiki/LoadBiocacheData" target="_blank">https://code.google.com/p/ala-portal/wiki/LoadBiocacheData</a>.
Precisely it's done inside the ubuntu box.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">After that I can see indexed records but for now it seems the mapping needs some configuration. I am still looking for configurations.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Did you get the map shown before?</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Cheers,</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Burke</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<div>
<div>
<p class="MsoNormal">On May 28, 2014, at 5:43 PM, sama <<a href="mailto:sama@gbif.es" target="_blank">sama@gbif.es</a>> wrote:</p>
</div>
<p class="MsoNormal"><br>
<br>
</p>
<p class="MsoNormal">-----BEGIN PGP SIGNED MESSAGE-----<br>
Hash: SHA1<br>
<br>
Dear Burke,<br>
<br>
Have you tried indexing a resource through their DwCA using<br>
biocache-store tool on Mac OS?<br>
<br>
Kind Regard.<br>
Sama<br>
- ------------------------------------------------------------<br>
Santiago Martínez de la Riva Vivanco<br>
GBIF.ES, Unidad de Coordinación<br>
Real Jardín Botánico CSIC<br>
Plaza de Murillo, 2<br>
28014 Madrid, Spain<br>
Tel: +34 91 4293917 x 273 - <a href="mailto:sama@gbif.es" target="_blank">sama@gbif.es</a> -
<a href="http://www.gbif.es" target="_blank">www.gbif.es</a> -<br>
<a href="https://twitter.com/smr_sama" target="_blank">https://twitter.com/smr_sama</a><br>
<br>
<br>
El 28/05/2014 17:34, Burke Chih-Jen Ko [GBIF] escribió:<br>
<br>
</p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Dear list members,<br>
(Sorry for cross-posting.)<br>
<br>
I would like to let you know that we've just updated these two pages on the wiki:<br>
<br>
1. Essential tools and environment configurations: <a href="http://dev.gbif.org/wiki/display/ALA/01+Essential+tools+and+environment+configurations" target="_blank">
http://dev.gbif.org/wiki/display/ALA/01+Essential+tools+and+environment+configurations</a><br>
2. Installation:<br>
<a href="http://dev.gbif.org/wiki/display/ALA/02+Installation" target="_blank">http://dev.gbif.org/wiki/display/ALA/02+Installation</a><br>
<br>
We are able to install the ALA portal demo by following these steps. Any suggestions on improving the documentation are highly appreciated!<br>
<br>
Cheers,<br>
<br>
Burke</p>
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