<div dir="ltr">Thanks Dave! I will test in our server.<div><br></div><div>Regards,<br><div><br></div><div><div style="color:rgb(0,0,0);font-family:'Times New Roman';font-size:16px"><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 id="7ead687c-0978-4f79-a9e0-57bfe0fad810" 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="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><br></div></div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">2014-05-09 2:14 GMT-03:00 <span dir="ltr"><<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a></span><span dir="ltr"></span><span dir="ltr">></span><span id="e7a5a497-7c88-425b-a072-fabc4f8301d3" class="GINGER_SOFTWARE_mark">:</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've spotted the problem:</div><div>
<div><br>
</div>
<div><span style="font-family:'Times New Roman';font-size:16px"><span id="4e5e7531-be49-476c-a89f-44abd75f7777" class="GINGER_SOFTWARE_mark">java</span></span><span style="font-family:'Times New Roman';font-size:16px"> -</span><span style="font-family:'Times New Roman';font-size:16px"><span id="22f72606-13e0-4add-b002-b28edcb8d306" class="GINGER_SOFTWARE_mark">cp</span></span><span style="font-family:'Times New Roman';font-size:16px"><span id="4a75abc7-7e29-448f-9587-fc75b014cbe4" class="GINGER_SOFTWARE_mark"> .</span></span><span style="font-family:'Times New Roman';font-size:16px"><span id="943d24b1-2e6a-4287-a339-d0d4fc431b5a" class="GINGER_SOFTWARE_mark">:</span></span><span style="font-family:'Times New Roman';font-size:16px"><span id="0be26191-8b84-489c-b4eb-415d27563864" class="GINGER_SOFTWARE_mark">biocache</span></span><span style="font-family:'Times New Roman';font-size:16px"><span id="aec7178e-72e0-4db3-aaf9-84d5ca51c519" class="GINGER_SOFTWARE_mark">.</span></span><span style="font-family:'Times New Roman';font-size:16px">jar
au.org.ala.util.DwcCSVLoader dr0 -l dataset-updated</span><span style="font-family:'Times New Roman';font-size:16px"><span id="1ccdc304-8200-445d-8bd7-2aecb42e0b8b" class="GINGER_SOFTWARE_mark">.</span></span><span style="font-family:'Times New Roman';font-size:16px"><span id="7c67a154-d113-49af-b5f1-60a787a74b17" class="GINGER_SOFTWARE_mark">csv</span></span><span style="font-family:'Times New Roman';font-size:16px"> -</span><span style="font-family:'Times New Roman';font-size:16px"><span id="3e3415b2-cde2-4b59-9677-a5eb90bf75d4" class="GINGER_SOFTWARE_mark">b</span></span><span style="font-family:'Times New Roman';font-size:16px"> true</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px"><br>
</span></div>
</div><div><span style="font-family:'Times New Roman';font-size:16px"><span id="63539b7e-fe59-4215-b801-7607938c616c" class="GINGER_SOFTWARE_mark">this</span> bypasses lookups against the <span id="efdd0b34-03bd-411c-a6ae-db11ab2b815e" class="GINGER_SOFTWARE_mark">collectory</span> for the metadata. </span></div>
<div><span style="font-family:'Times New Roman';font-size:16px"><br>
</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px">To load this dataset, you can use the <span id="841d1d13-fae1-4a0f-8d72-1308416a638c" class="GINGER_SOFTWARE_mark">biocache</span> <span id="9be71d43-6048-49c6-a27e-bb4cb2550557" class="GINGER_SOFTWARE_mark">commandline</span> tool like so:</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px"><br>
</span></div>
<div>
<p></p>
<p>$ <span id="4c4fee00-29f7-47e6-b55d-cdb40c0c373a" class="GINGER_SOFTWARE_mark">java</span> -<span id="7aa8c628-ed69-42bc-89c7-8c3afa4cd61f" class="GINGER_SOFTWARE_mark">cp</span> /usr/lib/<span id="9e3fea3d-2774-4527-af15-6b75c18cbe01" class="GINGER_SOFTWARE_mark">biocache</span><span id="cb03f060-05cd-4530-aeff-be4ec2f0ebbd" class="GINGER_SOFTWARE_mark">:</span>/usr/lib/<span id="70354894-3408-407c-9e52-45e69f4d5fb0" class="GINGER_SOFTWARE_mark">biocache</span>/<span id="1a43da94-8cf7-4edb-8920-4f55778a0e07" class="GINGER_SOFTWARE_mark">biocache</span>-store-1.1-assembly<span id="b809b1cc-da83-4485-807b-f2e310a682ae" class="GINGER_SOFTWARE_mark">.</span>jar -Xms2g -Xmx2g au.org.ala.biocache.cmd.CommandLineTool</p>
<p><br>
</p>
<p>----------------------------</p>
<p>| <span id="e591ea16-6657-4262-bc44-428c181d45f2" class="GINGER_SOFTWARE_mark">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 id="a7f7daa3-eb92-4e4a-94de-5e015be6c07e" class="GINGER_SOFTWARE_mark">biocache</span>> ingest dr8</p>
</div>
<div><span style="font-family:'Times New Roman';font-size:16px"><br>
</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px">This will:</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px"><br>
</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px">1) Retrieve the metadata from the configured instance of the <span id="764e5b14-277b-42a5-8347-403231dadc97" class="GINGER_SOFTWARE_mark">collectory</span></span></div>
<div><span style="font-family:'Times New Roman';font-size:16px">2) Load, process, sample (if there are layers configured and available) and index</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px"><br>
</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px">Cheers</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px"><br>
</span></div>
<div><span style="font-family:'Times New Roman';font-size:16px">Dave</span></div>
<div><br>
</div>
<div>
<div>
<div style="font-family:'Times New Roman';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 id="382b78b0-c415-42b1-8fc7-2b38803ff16d" class="GINGER_SOFTWARE_mark">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'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"><<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 id="41d459bc-59e6-4f0d-9b31-543fc732f096" class="GINGER_SOFTWARE_mark">:</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:'Times New Roman';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 id="022c1c52-ace2-4377-9c14-afbd28fb2266" class="GINGER_SOFTWARE_mark">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 "occurrenceID" to identify the records. It'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 id="568bc8be-8095-4210-bf59-340355b72653" class="GINGER_SOFTWARE_mark">java</span></span> -<span><span id="e896c804-985f-44ef-befe-671ed5bf543a" class="GINGER_SOFTWARE_mark">cp</span></span><span><span id="5f27ea9c-895e-43d4-a77d-61d749531c8b" class="GINGER_SOFTWARE_mark"> .</span></span><span><span id="6f774281-4974-4193-b8d4-beda39c66712" class="GINGER_SOFTWARE_mark">:</span></span><span><span id="41c27eb6-3c96-4a93-adc7-59989532a6cc" class="GINGER_SOFTWARE_mark">biocache</span></span><span><span id="cc8f3f65-b958-4d97-b889-9e550be9edc8" class="GINGER_SOFTWARE_mark">.</span></span>jar au.org.ala.util.DwcCSVLoader dr0 -l dataset.csv -<span><span id="279fa534-c234-40df-8385-dc865d0e5b32" class="GINGER_SOFTWARE_mark">b</span></span> true)</div>
<div><br>
</div>
<div><font color="#38761d">{<span><span id="aeb09f90-6efc-41f8-8436-61b90a319c5f" class="GINGER_SOFTWARE_mark">OccurrenceID</span></span>: 1, municipality: Sao Paulo,<span><span id="185dcc80-dfc3-4e0c-b129-828704bc8ef2" class="GINGER_SOFTWARE_mark"> ...</span></span>},</font></div>
<div><font color="#3d85c6">{<span><span id="ab6955ba-b7d7-473b-84fe-7ed081ffb054" class="GINGER_SOFTWARE_mark">OccurrenceID</span></span>: 2, municipality: Sao Paulo,<span><span id="6fc2b998-5249-481e-a295-c47e885b25f4" class="GINGER_SOFTWARE_mark"> ...</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 id="b8fbf9f0-1d42-4981-b800-ed5fa64abe71" class="GINGER_SOFTWARE_mark">java</span></span> -<span><span id="1d2ce095-6e4c-4e77-89e4-1ce15d5e74cc" class="GINGER_SOFTWARE_mark">cp</span></span><span><span id="5e409008-e82c-44bd-b965-829c078e42de" class="GINGER_SOFTWARE_mark"> .</span></span><span><span id="b262534d-dca4-439e-9724-aac544ad9f64" class="GINGER_SOFTWARE_mark">:</span></span><span><span id="57370913-a93d-426b-8331-41ff211c302c" class="GINGER_SOFTWARE_mark">biocache</span></span><span><span id="b7e32cdb-6186-448d-8391-80714b8dbb5e" class="GINGER_SOFTWARE_mark">.</span></span>jar au.org.ala.util.DwcCSVLoader dr0 -l dataset-updated<span><span id="43ace5c8-90dc-400a-8319-61a66d5ca4ae" class="GINGER_SOFTWARE_mark">.</span></span><span><span id="8f1f7ee1-3c14-4811-a8b6-377deff587bb" class="GINGER_SOFTWARE_mark">csv</span></span> -<span><span id="f9b691c3-832f-404a-bc5e-eeb955a17e63" class="GINGER_SOFTWARE_mark">b</span></span> true)</div>
<div>
<div><br>
</div>
<div><font color="#38761d">{<span><span id="432cab27-8a8e-4fac-8fe1-67443cbbdba0" class="GINGER_SOFTWARE_mark">OccurrenceID</span></span>: 1, </font><span style="color:rgb(56,118,29)">municipality</span><font color="#38761d">: Rio de Janeiro,<span><span id="10201118-e867-4a3b-89e9-6b3ca13b88e8" class="GINGER_SOFTWARE_mark"> ...</span></span>},</font></div>
<div><font color="#3d85c6">{<span><span id="932557b5-2e39-4789-95ee-f32dab6e1a8c" class="GINGER_SOFTWARE_mark">OccurrenceID</span></span>: 2, </font><span style="color:rgb(61,133,198)">municipality</span><font color="#3d85c6">: Rio de Janeiro,<span><span id="73df0294-6a03-4139-ac89-2ac915cf5fd2" class="GINGER_SOFTWARE_mark"> ...</span></span>},</font></div>
</div>
<div>{<span><span id="bb50d2b9-a576-4964-85da-d2f85bc474c9" class="GINGER_SOFTWARE_mark">OccurrenceID</span></span>: 3, municipality: Sao Paulo,<span><span id="f5bbe23f-bbae-4a31-ad31-f00313c7054d" class="GINGER_SOFTWARE_mark"> ...</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 id="813160d7-9cca-49ed-9b5b-bb97658d4eb7" class="GINGER_SOFTWARE_mark">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)">Sao Paulo</span><font color="#38761d">,<span><span id="87c626d1-9d51-4408-8401-22b9cfe0ae57" class="GINGER_SOFTWARE_mark"> ...</span></span>},</font></div>
<div><font color="#3d85c6">{<span><span id="0e653648-6db4-480f-a261-84719a6e744e" class="GINGER_SOFTWARE_mark">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 id="e8d2ecf9-e7df-4eed-8358-a3b8328762bc" class="GINGER_SOFTWARE_mark"> ...</span></span>},</font></div>
</div>
<div>
<div>
<div><font color="#38761d">{<span><span id="3ba91386-4d37-48c8-b8cc-adda46c867a7" class="GINGER_SOFTWARE_mark">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 de Janeiro</span><font color="#38761d">,<span><span id="174ab810-f77d-47b3-82fe-da6e125decb4" class="GINGER_SOFTWARE_mark"> ...</span></span>},</font></div>
<div><font color="#3d85c6">{<span><span id="e458e0e6-4d85-47d1-9364-eb93c14cb074" class="GINGER_SOFTWARE_mark">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 de Janeiro</span><font color="#3d85c6">,<span><span id="c2495ed7-4dc0-4fbe-a336-2ddf988e710c" class="GINGER_SOFTWARE_mark"> ...</span></span>}</font></div>
</div>
</div>
<div>{<span><span id="c0fa1ceb-d628-4826-97e6-c53d44ed5c20" class="GINGER_SOFTWARE_mark">OccurrenceID</span></span>: 3, municipality: Sao Paulo,<span><span id="ab26ca87-1f39-4ceb-b254-e3567e15510e" class="GINGER_SOFTWARE_mark"> ...</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 id="85b47ec7-7fbf-4901-9617-e38fdb9b0d64" class="GINGER_SOFTWARE_mark">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 de Janeiro</span><span style="color:rgb(56,118,29)">,<span><span id="403e23aa-1ad0-4f51-918c-1c584b21a08a" class="GINGER_SOFTWARE_mark"> ...</span></span>},</span><br>
</div>
<div>
<div><font color="#3d85c6">{<span><span id="033c87dc-ffe0-41a3-afa4-ada14af7e244" class="GINGER_SOFTWARE_mark">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 de Janeiro</span><font color="#3d85c6">,<span><span id="5f4f08f3-bbf0-4da0-9b94-5ea203cfc29c" class="GINGER_SOFTWARE_mark"> ...</span></span>}</font></div>
</div>
<div>{<span><span id="d9f02187-411b-4604-a472-a58333e78ad5" class="GINGER_SOFTWARE_mark">OccurrenceID</span></span>: 3, municipality: Sao Paulo,<span><span id="91618437-2fce-4701-8123-c516609c550f" class="GINGER_SOFTWARE_mark"> ...</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 id="b89ad43c-4002-4fe0-ad2f-79d58b5c3fba" class="GINGER_SOFTWARE_mark">on</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"><<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a></span><span dir="ltr"></span><span dir="ltr">></span><span id="f42c0a93-8582-4e81-b2aa-26e00c47b8dc" class="GINGER_SOFTWARE_mark">:</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 id="b428e028-bdce-430f-bbf2-d00c29f46b01" class="GINGER_SOFTWARE_mark">information</span> stored in the <span id="15d58b12-c4f2-4c9d-b848-214ebd0a656a" class="GINGER_SOFTWARE_mark">collectory</span>. See screenshot [1].</div>
<div><span style="font-size:10pt">By default, "<span id="16afab5e-2a20-4e17-8265-5fa1f0855b54" class="GINGER_SOFTWARE_mark">catalogNumber</span>" is <span id="c64785b5-9308-4313-9d2e-b1018965542c" class="GINGER_SOFTWARE_mark">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't recommended (e.g. <span id="3e672982-d1cf-4ee8-8013-d426eeac5223" class="GINGER_SOFTWARE_mark">scientificName</span>). To update the records, the process is to just re-load the dataset.</div>
<div><br>
</div>
<div>Automatically loaded - this <span id="3794be4a-36e2-47f3-a109-8474cc471b63" class="GINGER_SOFTWARE_mark">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:'Times New Roman';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 id="343639c8-99d7-4f92-aac3-16359a41089c" class="GINGER_SOFTWARE_mark">problems</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>occurrenceID</span> (I did set in the data resource configuration to use "OcurrenceID" to uniquely identify a record).</div>
<div><br>
</div>
<div>How can I update existing records in the database? For instance, the location'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 "Automatically loaded" and "Incremental Load". </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 id="17f42ae1-c04e-48ab-8844-7174c76f314b" class="GINGER_SOFTWARE_mark">on</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"><<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>></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 id="27e123ff-2cba-493b-aa12-51e56ea64b5a" class="GINGER_SOFTWARE_mark">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="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"><<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"></span><span dir="ltr">></span><span>:</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 id="2d2139dc-9d5d-478a-a1f8-f4e68138e7a9" class="GINGER_SOFTWARE_mark">.</span></span></span>zip
</b>and then running the following:</div>
<div>
<div><span><span><span id="b1843158-75e4-4135-ba64-aed19d3cbd48" class="GINGER_SOFTWARE_mark">s<b>udo</b></span><b></b><b></b></span><b></b><b></b><b></b></span><b> <span><span><span id="d53333ab-076e-492d-b869-2f1d8904e8b4" class="GINGER_SOFTWARE_mark">java</span></span></span> -<span><span><span id="fbc32824-3a94-4824-b2a0-d84c7b65a332" class="GINGER_SOFTWARE_mark">cp</span></span></span><span><span><span id="52c2a576-de65-466c-832b-03e25cfe6bc3" class="GINGER_SOFTWARE_mark"> .</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 id="ee877bed-681f-445e-b965-b0f97cadac23" class="GINGER_SOFTWARE_mark">collectory</span></span></span> to provide the <span>
<span><span id="5841726c-142a-4623-8a6f-574303e83944" class="GINGER_SOFTWARE_mark">dwca</span></span></span> the <span><span><span id="2a6f9b22-4766-45f4-822b-24a705ef17ab" class="GINGER_SOFTWARE_mark">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>"<span><span><span id="cdfb7a7e-e7a1-4afa-a130-d8a0414704d0" class="GINGER_SOFTWARE_mark">protocol</span></span></span>":"DwCA"</div>
<div>"<span><span><span id="941a4b83-3065-489d-9ded-b967d0f18e6e" class="GINGER_SOFTWARE_mark">termsForUniqueKey</span></span></span>"<span><span><span id="38fb1f4a-d98a-4b46-98ed-4cf25d114738" class="GINGER_SOFTWARE_mark">:</span></span></span>["<span><span>occurrenceID</span></span>"],</div>
<div><span>"url":"file:////data/collectory/upload/</span>1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b.zip<span>"</span></div>
<div><b><br>
</b></div>
<div>You could then load the resource by:</div>
<div>
<div><span><span><span id="b78efe24-3814-4f51-81be-717fac13b2cc" class="GINGER_SOFTWARE_mark">s<b>udo</b></span><b></b><b></b></span><b></b><b></b><b></b></span><b> <span><span><span id="5ad1ef2d-dcf5-4cce-a34f-d17eea0f5b15" class="GINGER_SOFTWARE_mark">java</span></span></span> -<span><span><span id="606983d0-0f15-4a5e-a780-593214e9238a" class="GINGER_SOFTWARE_mark">cp</span></span></span><span><span><span id="30513302-3045-47a6-aaf0-6e0801290bc6" class="GINGER_SOFTWARE_mark"> .</span></span></span><span><span><span id="fa94d872-fa75-49b7-b281-b2926a3f97c9" class="GINGER_SOFTWARE_mark">:</span></span></span><span><span><span id="159c35ac-0614-4da3-b501-4137ab969846" class="GINGER_SOFTWARE_mark">biocache</span></span></span><span><span><span id="09dd1659-5e43-45a1-95a7-97a2ef3f0b29" class="GINGER_SOFTWARE_mark">.</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 id="de8b785c-d0ac-403a-8d35-e8b729df29a5" class="GINGER_SOFTWARE_mark">issues please</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 <<a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a>><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 id="6b4273fe-1f0e-4bdc-8883-d778d16648c7" class="GINGER_SOFTWARE_mark">"<a href="mailto:ala-portal@lists.gbif.org" target="_blank">ala-portal@lists.gbif.org</a>" <<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><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 id="3ff7d0c2-04aa-4ecc-b756-e0d845c835ff" class="GINGER_SOFTWARE_mark">>,</span></span></span>
"dos Remedios, Nick (CES, Black Mountain)" <<a href="mailto:Nick.Dosremedios@csiro.au" target="_blank">Nick.Dosremedios@csiro.au</a><span><span><span id="0812b693-2cdc-4039-9584-d1cf26f412e4" class="GINGER_SOFTWARE_mark">>,</span></span></span> "Martin, Dave (CES, Black Mountain)" <<a href="mailto:David.Martin@csiro.au" target="_blank">David.Martin@csiro.au</a>><br>
<span style="font-weight:bold">Subject: </span>[Ala-portal] DwC-A loading <span><span><span id="625fb961-391f-4530-88b6-4239b070bc28" class="GINGER_SOFTWARE_mark">problems</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 "au.org.ala.util.DwCALoader", our system returns the error message
<font color="#ff0000">"Exception in thread "main" org<span><span><span id="d34529d3-895e-4650-b40c-c5a8b7470f94" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="6e93bfa4-0a5c-4904-85da-42aa4980d2bb" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="5cc0eddd-502a-4286-a148-bb468ca1e510" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="1b670d30-4303-4393-b5ea-4bfea97f46b3" class="GINGER_SOFTWARE_mark">dwc</span></span></span><span><span><span id="dae1bdb5-3130-439b-bd1b-f38d5dc993e0" class="GINGER_SOFTWARE_mark">.</span></span></span>text<span><span><span id="61297371-3249-4612-9279-3fb78b271ffa" class="GINGER_SOFTWARE_mark">.</span></span></span>UnkownDelimitersException: Unable
to detect field delimiter"</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 id="d8d15250-6864-4804-bdf1-411d98423724" class="GINGER_SOFTWARE_mark">tab</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 id="3842b0ae-fb90-4493-bf66-e698f870f03d" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="f1a28cd6-82d0-4768-866e-c552ef79bfed" class="GINGER_SOFTWARE_mark">ConfigModule</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 id="c75e45c9-83ac-4db4-bdfd-121a5ad5cd9a" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="8bf2231d-60a6-4d33-a053-3cdf2504a782" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span></span>] - Initialise SOLR</div>
<div>2014-04-28 01:44:03,103 INFO<span><span><span><span id="03760a14-1f57-411c-84ea-c25903e79ce2" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="55c4ec1b-8bca-41f6-8e47-26c81c1716d3" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span></span>] -
<span><span><span><span id="924711b4-734e-476e-970c-94cd69ae77cd" class="GINGER_SOFTWARE_mark">Initialise</span></span></span></span> name matching indexes</div>
<div>2014-04-28 01:44:03,605 INFO<span><span><span><span id="8dec92c4-d13d-4676-9346-5589bebacd2d" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="eb77c68c-4bd2-4333-8157-6522e6893b05" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span></span>] - Initialise persistence manager</div>
<div>2014-04-28 01:44:03,606 INFO<span><span><span><span id="571e3d03-801a-4d69-a6d3-ae91ff71069c" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="28ac912a-3ebb-4b06-9700-da15434b8c6d" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span></span>] - Configure complete</div>
<div>Loading archive /data/<span><span><span><span id="2d7c585e-f0e8-4a1a-98cd-67104bf1fc66" class="GINGER_SOFTWARE_mark">collectory</span></span></span></span>/upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b<span><span><span><span id="a29892aa-25b3-421a-b51a-1523690aa31c" class="GINGER_SOFTWARE_mark">.</span></span></span></span>zip for resource dr7 with unique terms List<span><span><span><span id="79426066-e509-45cf-acc4-358a3c6f5401" class="GINGER_SOFTWARE_mark">(</span></span></span></span><span><span><span><span id="f4ac6704-c6fc-48f7-a524-577e7c54a5aa" class="GINGER_SOFTWARE_mark">dwc</span></span></span></span><span><span><span><span id="d701c758-5a34-4da6-9acb-0a9454fc96fa" class="GINGER_SOFTWARE_mark">:</span></span></span></span><span><span><span>occurrenceID</span></span></span>)
stripping spaces false incremental false testing <span><span><span><span id="895f3397-0802-4c1f-9cc4-08b98fc913bf" class="GINGER_SOFTWARE_mark">false</span></span></span></span></div>
<div><b>Exception in thread "main" org<span><span><span><span id="59cf835c-740a-4e05-9b0b-afe37f7e846c" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="f834ddbb-8e8c-4172-88da-104147c070d6" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="ce11bba9-17fe-4bf1-9aa0-e73ae7a237b8" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="77cb6fde-be9f-4684-8554-677a0da223a7" class="GINGER_SOFTWARE_mark">dwc</span></span></span></span><span><span><span><span id="869bbcbc-54e6-4227-89f0-43350bdff674" class="GINGER_SOFTWARE_mark">.</span></span></span></span>text<span><span><span><span id="0dd4f3fa-bf9d-4297-900f-df75254327ef" class="GINGER_SOFTWARE_mark">.</span></span></span></span>UnkownDelimitersException:
Unable to detect field delimiter</b></div>
<div> <span><span><span><span id="da9f3cab-5993-4fc7-bb3b-0b3f31cc24ca" class="GINGER_SOFTWARE_mark">at</span></span></span></span> org<span><span><span><span id="7cda7a7d-a5e9-4963-ab74-b06aa2f4c591" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="19498f56-3d0a-4ead-b2bf-3d733946bfa7" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="9b5d2bf6-36da-4715-9752-a0e87fa9bb03" class="GINGER_SOFTWARE_mark">.</span></span></span></span>file<span><span><span><span id="a5ba034a-89b8-4689-ad3d-08b1fa175032" class="GINGER_SOFTWARE_mark">.</span></span></span></span>CSVReaderFactory<span><span><span><span id="68b6ed78-d96f-44c8-a3d0-27a9bcae0de2" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="4a6db4ca-e386-476e-9ede-285181f0d839" class="GINGER_SOFTWARE_mark">buildArchiveFile</span></span></span></span><span><span><span><span id="6ff6dee4-0cb6-46d0-8695-5173aae71b51" class="GINGER_SOFTWARE_mark">(</span></span></span></span>CSVReaderFactory.java<span><span><span><span id="bc5b2093-2b51-405a-b990-fb86bff50942" class="GINGER_SOFTWARE_mark">:</span></span></span></span>129)</div>
<div> <span><span><span><span id="03f45395-7bd7-4978-aa7d-01f8ceed58f9" class="GINGER_SOFTWARE_mark">at</span></span></span></span> org<span><span><span><span id="65e799ce-dd70-40ac-9692-eb36cc12bd9b" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="49bb266f-a73b-4daf-9f56-bc1bac8a0fa4" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="3d39f0aa-c1a2-4511-bf3e-6f8011d5def1" class="GINGER_SOFTWARE_mark">.</span></span></span></span>file<span><span><span><span id="f4d92d22-02aa-46c7-9ba3-bf5e6adae8d4" class="GINGER_SOFTWARE_mark">.</span></span></span></span>CSVReaderFactory<span><span><span><span id="f11a73df-0067-4ed9-af5d-29a8717d47de" class="GINGER_SOFTWARE_mark">.</span></span></span></span>build<span><span><span><span id="25f68c1d-ab2e-4a18-b222-149cb824f2d7" class="GINGER_SOFTWARE_mark">(</span></span></span></span>CSVReaderFactory.java<span><span><span><span id="946ebfbf-ae62-46a2-8b83-435f0ae234d6" class="GINGER_SOFTWARE_mark">:</span></span></span></span>46)</div>
<div> <span><span><span><span id="a2c45a6f-2436-4e00-8948-f3910be5dd00" class="GINGER_SOFTWARE_mark">at</span></span></span></span> org<span><span><span><span id="e38d5ef2-d1e4-4ffe-9afa-7278f26884a3" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="b7ec2709-3fb8-45e3-ac78-5cbfb9e1e0ea" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="577b59a9-c439-4469-a0cc-89b73bc0c305" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="8c7ef28c-d8d0-408d-a6f4-7ab96f1214e0" class="GINGER_SOFTWARE_mark">dwc</span></span></span></span><span><span><span><span id="80e61ec3-e5d0-4f25-b3c9-e83740e57031" class="GINGER_SOFTWARE_mark">.</span></span></span></span>text<span><span><span><span id="4fb59c58-3e3a-4c77-82d5-147d45750c66" class="GINGER_SOFTWARE_mark">.</span></span></span></span>ArchiveFactory<span><span><span><span id="1d1cebfa-4521-45b5-82d1-39636067edc1" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="95e9f547-1b57-4a72-a7e9-ed8189ef8e49" class="GINGER_SOFTWARE_mark">readFileHeaders</span></span></span></span><span><span><span><span id="33fd50ce-3ae9-4f19-a960-b6205e36f55e" class="GINGER_SOFTWARE_mark">(</span></span></span></span>ArchiveFactory.java<span><span><span><span id="c0f496cb-1c2a-4914-ae1a-3875b7fae11a" class="GINGER_SOFTWARE_mark">:</span></span></span></span>344)</div>
<div> <span><span><span><span id="51e2abab-c23a-4d05-b5b8-5e80713dd47a" class="GINGER_SOFTWARE_mark">at</span></span></span></span> org<span><span><span><span id="615af429-8b97-4dce-a1a3-cfa79500eb0c" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="45acec78-136d-4b8f-9528-2c8ae90ca8bd" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="d5049078-de8d-4ae5-9b81-86ccbf08008a" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="7b661992-a24c-4aa4-a341-cb2e2e7f41f3" class="GINGER_SOFTWARE_mark">dwc</span></span></span></span><span><span><span><span id="7c9273d7-6f7d-4fcb-ab71-49ec70464076" class="GINGER_SOFTWARE_mark">.</span></span></span></span>text<span><span><span><span id="eb10c962-77a6-4a28-ad91-7988d81d8c76" class="GINGER_SOFTWARE_mark">.</span></span></span></span>ArchiveFactory<span><span><span><span id="37db6164-3e1b-406a-a4f7-37f426bead6a" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="42aa859b-607d-44c3-bd57-af65f61f1e9c" class="GINGER_SOFTWARE_mark">openArchive</span></span></span></span><span><span><span><span id="6d28568f-2a45-43b7-88e8-a6869fbdd4e2" class="GINGER_SOFTWARE_mark">(</span></span></span></span>ArchiveFactory.java<span><span><span><span id="198b2872-d557-4fdf-abec-34dcbbf82c08" class="GINGER_SOFTWARE_mark">:</span></span></span></span>289)</div>
<div> <span><span><span><span id="d9dae6cc-23a0-4253-8443-53ee74fb8673" class="GINGER_SOFTWARE_mark">at</span></span></span></span> au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129)</div>
<div> <span><span><span><span id="d1ad08ce-3de6-475f-9136-cf2f1987516c" class="GINGER_SOFTWARE_mark">at</span></span></span></span> au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106)</div>
<div> <span><span><span><span id="583fb665-3161-4bd1-93e0-b5c9ea979599" class="GINGER_SOFTWARE_mark">at</span></span></span></span> au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52)</div>
<div> <span><span><span><span id="6f0c8a13-e6f6-4db7-9748-bcae8f1db6bb" class="GINGER_SOFTWARE_mark">at</span></span></span></span> au.org.ala.util.DwCALoader.main(DwCALoader.scala)</div>
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<div><b><i><span><span><span><span id="5587243e-35c0-4c07-ad6c-a5e49b06ff74" class="GINGER_SOFTWARE_mark">comma</span></span></span></span>-delimited file test</i></b><br>
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<div>poliusp@poliusp-VirtualBox:~/dev/biocache$ <b>sudo java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7 -l ./<span><span><span><span id="a8269856-6b10-42fe-aa46-f03a67652468" class="GINGER_SOFTWARE_mark">dwca</span></span></span></span>-teste3<span><span><span><span id="11fa74d0-8ad1-4997-9372-de45bc6d4ee4" class="GINGER_SOFTWARE_mark">.</span></span></span></span>zip</b></div>
<div>2014-04-28 01:56:04,683 INFO<span><span><span><span id="e906e253-16e7-4f68-bf83-8f40c8aab0c7" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="443ab10a-f272-49c4-837f-c73417038062" class="GINGER_SOFTWARE_mark">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 id="097ec5d6-10e1-4cfc-bf1d-a844c37821c9" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="68689ec5-d8dd-4903-9d82-54a5864f3ef0" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span></span>] - Initialise SOLR</div>
<div>2014-04-28 01:56:04,951 INFO<span><span><span><span id="8f0c4512-fb7e-461a-bf12-0f3e60298ed0" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="87174aea-b045-414d-bca9-573dae55a144" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span></span>] -
<span><span><span><span id="0b32a6f1-013a-4935-b2dc-cedfe579a20b" class="GINGER_SOFTWARE_mark">Initialise</span></span></span></span> name matching indexes</div>
<div>2014-04-28 01:56:05,437 INFO<span><span><span><span id="f37b41c9-c976-4504-b154-ecd694449e27" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="4b6c2d7e-62d6-4e85-adb0-0e5fa56aa57c" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span></span>] - Initialise persistence manager</div>
<div>2014-04-28 01:56:05,438 INFO<span><span><span><span id="f9455da0-0d96-4ff6-a576-d5d7bd84278c" class="GINGER_SOFTWARE_mark"> :</span></span></span></span> [<span><span><span><span id="bb04a0ce-efa3-431d-b192-8a5609cb5307" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span></span>] - Configure complete</div>
<div>Loading archive<span><span><span><span id="6f9a6305-9dce-4079-903c-6a681d1b5eda" class="GINGER_SOFTWARE_mark"> .</span></span></span></span>/<span><span><span><span id="9277a692-4bc1-46b4-97eb-4925d65e0323" class="GINGER_SOFTWARE_mark">dwca</span></span></span></span>-teste3<span><span><span><span id="c4bdc6b2-8cc5-4309-b14c-9a369706ddc2" class="GINGER_SOFTWARE_mark">.</span></span></span></span>zip for resource dr7 with unique terms List<span><span><span><span id="60890105-4d0c-4a6a-a606-6a19536c2266" class="GINGER_SOFTWARE_mark">(</span></span></span></span><span><span><span><span id="ce0883e4-0dbd-4d9b-bbdc-cc8993618d6a" class="GINGER_SOFTWARE_mark">dwc</span></span></span></span><span><span><span><span id="a521be2a-5b16-4cca-ba54-f512a9a10d29" class="GINGER_SOFTWARE_mark">:</span></span></span></span><span><span><span>occurrenceID</span></span></span>)
stripping spaces false incremental false testing <span><span><span><span id="c20fe3c5-3f00-41ca-ba87-972343d70086" class="GINGER_SOFTWARE_mark">false</span></span></span></span></div>
<div><b>Exception in thread "main" org<span><span><span><span id="59c33ed8-af11-42bb-b578-8bb15f5bf5ec" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="0a02a0e8-d5c7-4384-a919-cdeffaee65d0" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="a4920d2e-ef9c-43a5-a712-4082f393d7d2" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="ae320078-46c9-4b8b-b79b-7a2e5b9ab935" class="GINGER_SOFTWARE_mark">dwc</span></span></span></span><span><span><span><span id="0b0dc705-ff3c-463b-b10a-db48e1bdc52d" class="GINGER_SOFTWARE_mark">.</span></span></span></span>text<span><span><span><span id="8cfa4e73-99c6-453c-986a-e8beec013622" class="GINGER_SOFTWARE_mark">.</span></span></span></span>UnkownDelimitersException:
Unable to detect field delimiter</b></div>
<div> <span><span><span><span id="f77c3700-50b3-4724-96f2-b91c97a94a21" class="GINGER_SOFTWARE_mark">at</span></span></span></span> org<span><span><span><span id="807ff0de-a94a-4db9-8e04-3e2f0cab5090" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="e9bc2038-5511-4318-a510-12047e83efd3" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="0d4f6fa3-6d1b-4dc1-b1a7-145b944e8651" class="GINGER_SOFTWARE_mark">.</span></span></span></span>file<span><span><span><span id="02884ab6-f941-4798-a948-0deec870f609" class="GINGER_SOFTWARE_mark">.</span></span></span></span>CSVReaderFactory<span><span><span><span id="54a623ab-3241-432f-8c95-3510db0239dc" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="2a4bd3e2-1186-4dbe-80e1-936ecb94ca50" class="GINGER_SOFTWARE_mark">buildArchiveFile</span></span></span></span><span><span><span><span id="1ae62872-fbd3-4f5f-8d35-1b8757133c26" class="GINGER_SOFTWARE_mark">(</span></span></span></span>CSVReaderFactory.java<span><span><span><span id="7e38dc95-1ab4-41f0-ae86-73a2dec7c218" class="GINGER_SOFTWARE_mark">:</span></span></span></span>129)</div>
<div> <span><span><span><span id="5f4af570-30fe-4251-adda-63445830757b" class="GINGER_SOFTWARE_mark">at</span></span></span></span> org<span><span><span><span id="e4efae0a-9efc-4596-b618-b087e2dc90f4" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="1ec21a4d-a18e-49ad-96ff-d86f5e1a4909" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="bb285b8a-1eb3-46df-a959-9c2921630eb0" class="GINGER_SOFTWARE_mark">.</span></span></span></span>file<span><span><span><span id="6bf15d72-b3d1-4363-aa90-5d779457d0d5" class="GINGER_SOFTWARE_mark">.</span></span></span></span>CSVReaderFactory<span><span><span><span id="6071ddfc-21e5-47c1-a641-6a8a43cfcb8a" class="GINGER_SOFTWARE_mark">.</span></span></span></span>build<span><span><span><span id="2a228fcb-e03c-4ac9-99ce-6b5d3515b06b" class="GINGER_SOFTWARE_mark">(</span></span></span></span>CSVReaderFactory.java<span><span><span><span id="ed1c78c3-ae0f-457b-af28-534e0e1d8c38" class="GINGER_SOFTWARE_mark">:</span></span></span></span>46)</div>
<div> <span><span><span><span id="92ceb54b-cd4e-4a04-a1e8-0f810dec1525" class="GINGER_SOFTWARE_mark">at</span></span></span></span> org<span><span><span><span id="ed9a0bc1-6855-460d-8a0b-1a2033c374e9" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="bff6e44b-ebb9-4d2e-8498-2932e9d4a1e1" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="6a267fc7-aa57-4c5b-b39f-6ef036079c29" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="f54cbf5c-f451-4409-83e5-0bae01459102" class="GINGER_SOFTWARE_mark">dwc</span></span></span></span><span><span><span><span id="ac16569e-88e5-4869-9687-9aa103886c0f" class="GINGER_SOFTWARE_mark">.</span></span></span></span>text<span><span><span><span id="d07c5bda-fc10-4390-b7d2-e4ede88b23ab" class="GINGER_SOFTWARE_mark">.</span></span></span></span>ArchiveFactory<span><span><span><span id="69810a9d-1aa2-4182-a37d-6b4702bc9734" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="d67d0eb9-8651-499f-911a-13ec311e693a" class="GINGER_SOFTWARE_mark">readFileHeaders</span></span></span></span><span><span><span><span id="4dcd3ca0-5266-49c5-abfe-3f01a82467b6" class="GINGER_SOFTWARE_mark">(</span></span></span></span>ArchiveFactory.java<span><span><span><span id="14c99f52-91c6-42e1-a3c7-be1fe64e133b" class="GINGER_SOFTWARE_mark">:</span></span></span></span>344)</div>
<div> <span><span><span><span id="8a70bd87-249f-4289-9a7c-d64d41a8fb29" class="GINGER_SOFTWARE_mark">at</span></span></span></span> org<span><span><span><span id="6401b2c0-4c6e-4992-97d5-33bb6561ca2e" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="a8230ed5-f93b-4ff8-88ef-bb74b2e7616d" class="GINGER_SOFTWARE_mark">gbif</span></span></span></span><span><span><span><span id="5aee4826-e046-47c0-92ec-11e49d9a6b0a" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="891a2948-db6b-4ff7-bf7a-7cb36a91c611" class="GINGER_SOFTWARE_mark">dwc</span></span></span></span><span><span><span><span id="0513582b-ed5b-4399-9247-32af57731e7d" class="GINGER_SOFTWARE_mark">.</span></span></span></span>text<span><span><span><span id="75dd9dae-b98a-4b15-a90d-a81258fa5c7c" class="GINGER_SOFTWARE_mark">.</span></span></span></span>ArchiveFactory<span><span><span><span id="322b6eaa-d1bd-4f1f-814b-c953db48b4f3" class="GINGER_SOFTWARE_mark">.</span></span></span></span><span><span><span><span id="1af82e93-e4d6-41eb-a1a8-be192ca4131a" class="GINGER_SOFTWARE_mark">openArchive</span></span></span></span><span><span><span><span id="ca10929d-255c-4e28-8cc3-db310c854a35" class="GINGER_SOFTWARE_mark">(</span></span></span></span>ArchiveFactory.java<span><span><span><span id="6ca1cc1a-9a8b-432e-882e-46c8b0d258d4" class="GINGER_SOFTWARE_mark">:</span></span></span></span>289)</div>
<div> <span><span><span><span id="434f9467-8baf-48c4-b855-c82406d40280" class="GINGER_SOFTWARE_mark">at</span></span></span></span> au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129)</div>
<div> <span><span><span><span id="7541951c-c7cb-4214-8c38-4fac4f3af058" class="GINGER_SOFTWARE_mark">at</span></span></span></span> au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106)</div>
<div> <span><span><span><span id="e16364eb-4849-4e79-b7ce-fdaa4cbb363c" class="GINGER_SOFTWARE_mark">at</span></span></span></span> au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52)</div>
<div> <span><span><span><span id="1fc7358e-d2e2-4a39-8600-ca7246f012f3" class="GINGER_SOFTWARE_mark">at</span></span></span></span> au.org.ala.util.DwCALoader.main(DwCALoader.scala)</div>
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<div>Thanks!</div>
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<div>Regards.</div>
-- <br>
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<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 id="41c8eb06-3ea0-43ba-8690-c71642910441" class="GINGER_SOFTWARE_mark">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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