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<div>Thanks Daniel. Natasha has now left the ALA.</div>
<div><br>
</div>
<div>The uniqueness of records is determined by information stored in the collectory. See screenshot [1].</div>
<div><span style="font-size: 10pt;">By default, "catalogNumber" is used but 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. scientificName). To update the records, the process is to just re-load the dataset.</div>
<div><br>
</div>
<div>Automatically loaded - this isnt 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" target="_blank" style="font-size: 10pt;">http://bit.ly/1g72HFN</a></div>
<div><br>
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<hr tabindex="-1">
<div id="divRpF800657" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> Daniel Lins [daniel.lins@gmail.com]<br>
<b>Sent:</b> 05 May 2014 15:39<br>
<b>To:</b> Quimby, Natasha (CES, Black Mountain)<br>
<b>Cc:</b> ala-portal@lists.gbif.org; dos Remedios, Nick (CES, Black Mountain); Martin, Dave (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">
<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 id="2da6abc2-7224-4434-bec0-b1dfcb70dcb8" class="GINGER_SOFTWARE_mark">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 id="4f856dc0-aaa6-4d32-a447-68331077611c" 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>
<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 class=""><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 id="5fff3558-6579-4235-bd3f-d122b055279f" 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="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>:</span><span></span><span></span><span></span>
<div>
<div class="h5"><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 id="db4ef583-61b0-4101-a226-4eaff10e4eaa" class="GINGER_SOFTWARE_mark">.</span></span>zip
</b>and then running the following:</div>
<div>
<div><span><span id="eb8c9149-29c1-49e0-a264-581da0c0a2f4" class="GINGER_SOFTWARE_mark">s<b>udo</b></span><b></b><b></b><b></b></span><b>
<span><span id="24a124ab-ec4f-482b-bede-7166ad3a666e" class="GINGER_SOFTWARE_mark">java</span></span> -<span><span id="5d05d9a7-3093-44fa-bf84-c69ab2912907" class="GINGER_SOFTWARE_mark">cp</span></span><span><span id="cbafc5ba-7467-4ec5-9eac-fd2db57e3272" class="GINGER_SOFTWARE_mark">
.</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 id="2c5a3bf4-f2c5-4a6e-b666-992c3248737f" class="GINGER_SOFTWARE_mark">collectory</span></span> to provide the
<span><span id="1d70117f-c82a-4804-bd3d-3a23680df91c" class="GINGER_SOFTWARE_mark">dwca</span></span> the
<span><span id="ba3bd8f7-a236-49be-9ea7-6865dcd5785b" class="GINGER_SOFTWARE_mark">biocache</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 id="30cb06f5-0e9b-494d-82a2-afb9499a6411" class="GINGER_SOFTWARE_mark">protocol</span></span>":"DwCA"</div>
<div>"<span><span id="4be6319b-d398-46a6-a391-1458f85bb409" class="GINGER_SOFTWARE_mark">termsForUniqueKey</span></span>"<span><span id="170cc500-ac54-49f1-aecf-b0cea60e62ab" class="GINGER_SOFTWARE_mark">:</span></span>["<span><span id="929fd25e-0e50-4ca2-ad49-e3a447988118" class="GINGER_SOFTWARE_mark">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 id="01b108a9-c4b6-40a6-ae38-37924bf1971a" class="GINGER_SOFTWARE_mark">s<b>udo</b></span><b></b><b></b><b></b></span><b>
<span><span id="e669075b-d838-4ab7-a691-80d8f1bd407e" class="GINGER_SOFTWARE_mark">java</span></span> -<span><span id="3c544c28-d3c6-42af-8849-54215b30dcc4" class="GINGER_SOFTWARE_mark">cp</span></span><span><span id="09750c39-4db5-4b46-b5f5-c52e716859a8" class="GINGER_SOFTWARE_mark">
.</span></span><span><span id="6be21e55-4133-4f8f-9de1-e3e4ee4c6166" class="GINGER_SOFTWARE_mark">:</span></span><span><span id="3241a6b9-cadd-42e8-8836-223cbd653c75" class="GINGER_SOFTWARE_mark">biocache</span></span><span><span id="384d46c2-4c6b-4a67-a6a8-8ac9fecb36cc" class="GINGER_SOFTWARE_mark">.</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 id="1cc06f79-5925-4100-aad1-8f7cf14f36ea" class="GINGER_SOFTWARE_mark">issues please</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 id="d142bdf2-f96a-42b7-88e1-e8cefcd1f618" 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><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 id="e6f8a56d-8c21-486c-af4c-c885beb95e31" class="GINGER_SOFTWARE_mark">>,</span></span>
"dos Remedios, Nick (CES, Black Mountain)" <<a href="mailto:Nick.Dosremedios@csiro.au" target="_blank">Nick.Dosremedios@csiro.au</a><span><span id="48d64cc9-a03d-4b73-af00-d6ffdbc5364c" class="GINGER_SOFTWARE_mark">>,</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 id="d0b210b6-c574-43b9-91d8-3262eeff2c24" class="GINGER_SOFTWARE_mark">problems</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 id="25766291-be9e-40c9-a4ff-54807e7f9071" class="GINGER_SOFTWARE_mark">.</span></span><span><span id="328d125f-67c4-4b68-a34e-5a5dcf47768b" class="GINGER_SOFTWARE_mark">gbif</span></span><span><span id="4651f934-9d85-4aca-8efb-00831623a1fd" class="GINGER_SOFTWARE_mark">.</span></span><span><span id="a7d524dd-bc64-44d8-902d-78e185258063" class="GINGER_SOFTWARE_mark">dwc</span></span><span><span id="8e7f8793-95dd-43b0-81cc-a9692a1a2c41" class="GINGER_SOFTWARE_mark">.</span></span>text<span><span id="9faf6469-e38f-40ec-858c-92a0249c1273" class="GINGER_SOFTWARE_mark">.</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 id="8e5e9bd5-33b6-4438-9a53-b73a03279a8e" class="GINGER_SOFTWARE_mark">tab</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 id="7a38c9ea-b4dc-4a2c-8b96-1c28892f30d7" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="3359bed1-a764-4335-82c1-fcc755b54b2e" class="GINGER_SOFTWARE_mark">ConfigModule</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 id="a2ed82d4-5a4a-4ed6-9d15-1438cc3231f1" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="0fb4ae42-4999-456c-a60a-57a89986e1fa" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span>]
- Initialise SOLR</div>
<div>2014-04-28 01:44:03,103 INFO<span><span><span id="d279b2ec-bda0-47dd-afd7-4b516dedb2e7" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="8cfaa28e-5ae3-4937-85fc-05de5674686f" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span>]
- <span><span><span id="f90a7bed-90e8-47b1-8e5d-110cfa59d584" class="GINGER_SOFTWARE_mark">Initialise</span></span></span> name matching indexes</div>
<div>2014-04-28 01:44:03,605 INFO<span><span><span id="d9ee7ccc-d8ec-4e1d-82c3-fe7982790f69" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="3f668e37-52e3-462a-8b92-c2d26732f6a2" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span>]
- Initialise persistence manager</div>
<div>2014-04-28 01:44:03,606 INFO<span><span><span id="c05a49a4-1ec1-464e-8acf-ad4e1a503ca7" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="1a79bf64-6cff-40d0-82d9-e13144212e86" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span>]
- Configure complete</div>
<div>Loading archive /data/<span><span><span id="ad475a92-5e7f-4371-a13b-74380a0a3689" class="GINGER_SOFTWARE_mark">collectory</span></span></span>/upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b<span><span><span id="e71aa1e5-238d-4cbe-a934-021f28c2ce8b" class="GINGER_SOFTWARE_mark">.</span></span></span>zip
for resource dr7 with unique terms List<span><span><span id="e50d658a-197e-4d7f-9416-6c19573c955d" class="GINGER_SOFTWARE_mark">(</span></span></span><span><span><span id="ff98d02d-c5d3-4beb-a0b8-306abb035c5a" class="GINGER_SOFTWARE_mark">dwc</span></span></span><span><span><span id="bffec54e-dfb9-4431-8a27-b1e4ee7482dd" class="GINGER_SOFTWARE_mark">:</span></span></span><span><span><span id="f5ccd242-e96c-4a4a-a41d-05857affb0de" class="GINGER_SOFTWARE_mark">occurrenceID</span></span></span>)
stripping spaces false incremental false testing <span><span><span id="8f0cb056-91c4-4c7e-b393-07f18152fec0" class="GINGER_SOFTWARE_mark">false</span></span></span></div>
<div><b>Exception in thread "main" org<span><span><span id="dc2fea1c-7af1-4a32-9c55-6e0c9a94eeaa" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="490c45c4-ce57-46e2-8e23-1907a9c8f20a" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="e6d07bdd-a404-4806-a0d1-fb6e92d52958" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="f6ebb257-1d48-4473-a318-e4011cbf6607" class="GINGER_SOFTWARE_mark">dwc</span></span></span><span><span><span id="72dc2c5d-0c7b-4f3c-8107-f37d1b2dc719" class="GINGER_SOFTWARE_mark">.</span></span></span>text<span><span><span id="42eb144b-5d51-4ee9-988e-4ea435f85fde" class="GINGER_SOFTWARE_mark">.</span></span></span>UnkownDelimitersException:
Unable to detect field delimiter</b></div>
<div> <span><span><span id="cc81dca2-ad61-4d9a-b3f0-1b1e9ef459f8" class="GINGER_SOFTWARE_mark">at</span></span></span> org<span><span><span id="2eb91f85-282f-4485-b40c-868d07202aa1" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="0797f39f-8f1b-4b65-a6b9-df0e19a789be" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="a0babe8c-327b-472d-b369-32de73a20278" class="GINGER_SOFTWARE_mark">.</span></span></span>file<span><span><span id="846d12cc-ee72-4281-86e5-b8b2a29095df" class="GINGER_SOFTWARE_mark">.</span></span></span>CSVReaderFactory<span><span><span id="1fff87f5-7a4d-4bc6-8ce9-ebf3106b7b99" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="b798a9c3-360c-4006-8088-72377d681623" class="GINGER_SOFTWARE_mark">buildArchiveFile</span></span></span><span><span><span id="b314e14d-b263-434b-b7ee-2e90ac63cf45" class="GINGER_SOFTWARE_mark">(</span></span></span>CSVReaderFactory.java<span><span><span id="31848607-16e7-4c52-9853-30c64a316158" class="GINGER_SOFTWARE_mark">:</span></span></span>129)</div>
<div> <span><span><span id="848b81ab-5ee5-4a86-a1b5-0ddfd629f081" class="GINGER_SOFTWARE_mark">at</span></span></span> org<span><span><span id="8ccde061-b1dc-4988-940e-acdee9a01bf1" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="d022b748-965b-476d-8dd2-575642db2b12" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="7d317216-ef7d-48b6-ac89-29ae8c50b30e" class="GINGER_SOFTWARE_mark">.</span></span></span>file<span><span><span id="46aa9f03-55d8-4840-8b46-8b5e5c6aef9c" class="GINGER_SOFTWARE_mark">.</span></span></span>CSVReaderFactory<span><span><span id="0013e280-a701-49b2-8ea5-c6ac2c2de9fa" class="GINGER_SOFTWARE_mark">.</span></span></span>build<span><span><span id="4b1c4d74-5fda-4e3d-aad2-2db2fcfc30f6" class="GINGER_SOFTWARE_mark">(</span></span></span>CSVReaderFactory.java<span><span><span id="bc9da423-d92d-4f32-88be-820ac87a654d" class="GINGER_SOFTWARE_mark">:</span></span></span>46)</div>
<div> <span><span><span id="182bf3ce-56bb-4cb9-9c47-056baba048af" class="GINGER_SOFTWARE_mark">at</span></span></span> org<span><span><span id="7accc243-6949-436d-96fd-9fc376881a2d" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="f6ad0e1d-b459-4498-bc2b-2f68221b5aea" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="7d1cb347-94f1-45b1-86a5-2c250366eda0" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="00343c07-cff9-4df7-a08b-bb2794eee88d" class="GINGER_SOFTWARE_mark">dwc</span></span></span><span><span><span id="7487c6ff-7963-4915-8dd2-e25afa3c08f4" class="GINGER_SOFTWARE_mark">.</span></span></span>text<span><span><span id="bec315c7-8fa7-4f11-b8b1-7d3622df146f" class="GINGER_SOFTWARE_mark">.</span></span></span>ArchiveFactory<span><span><span id="a496be22-6bf1-4e4a-ab5e-6db7b43e6c09" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="e366f1ed-e78d-40de-8c4c-b8e8a1744563" class="GINGER_SOFTWARE_mark">readFileHeaders</span></span></span><span><span><span id="e34df81d-86a4-4c4d-9700-e20a5690e270" class="GINGER_SOFTWARE_mark">(</span></span></span>ArchiveFactory.java<span><span><span id="613d2e9b-944c-459d-b534-1db25af73253" class="GINGER_SOFTWARE_mark">:</span></span></span>344)</div>
<div> <span><span><span id="2a300edd-51d9-4403-b9ec-a753fcbe9020" class="GINGER_SOFTWARE_mark">at</span></span></span> org<span><span><span id="6bcc8924-87d2-4d36-8611-f33c35de1fbb" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="4273c466-065d-4503-bed5-b6265cd4ae53" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="6ba352ee-1021-4631-a314-126f6f5411d3" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="be7630a5-78c4-448a-88f4-5d6d1584708b" class="GINGER_SOFTWARE_mark">dwc</span></span></span><span><span><span id="6e532d2a-f082-44b1-97c9-33de3cedc77d" class="GINGER_SOFTWARE_mark">.</span></span></span>text<span><span><span id="5f448aac-a627-4e51-b392-da4b9849d499" class="GINGER_SOFTWARE_mark">.</span></span></span>ArchiveFactory<span><span><span id="27a07857-f830-45f6-a2bf-f116aa059e28" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="e88cf76b-abe4-49b2-965d-104a32be79c3" class="GINGER_SOFTWARE_mark">openArchive</span></span></span><span><span><span id="faa8933e-47d7-4163-a580-5c47dabd359d" class="GINGER_SOFTWARE_mark">(</span></span></span>ArchiveFactory.java<span><span><span id="716e61ed-7f14-4c9f-8360-62f4474c0231" class="GINGER_SOFTWARE_mark">:</span></span></span>289)</div>
<div> <span><span><span id="41fc9c73-4e0a-46aa-a98b-bd1ed21a7983" class="GINGER_SOFTWARE_mark">at</span></span></span> au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129)</div>
<div> <span><span><span id="1d3c679f-579c-4848-8513-2e295e2019cb" class="GINGER_SOFTWARE_mark">at</span></span></span> au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106)</div>
<div> <span><span><span id="cef54cf3-47de-4117-b429-3210f59913b6" class="GINGER_SOFTWARE_mark">at</span></span></span> au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52)</div>
<div> <span><span><span id="b6e2b6b2-0a91-462f-a7a9-dbb5aceea2b1" class="GINGER_SOFTWARE_mark">at</span></span></span> au.org.ala.util.DwCALoader.main(DwCALoader.scala)</div>
<div><br>
</div>
<div><br>
</div>
<div><b><i><span><span><span id="aee7286a-bf16-4a82-960a-7bbefd5a8ba9" class="GINGER_SOFTWARE_mark">comma</span></span></span>-delimited file test</i></b><br>
</div>
<div><br>
</div>
<div>
<div>poliusp@poliusp-VirtualBox:~/dev/biocache$ <b>sudo java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7 -l ./<span><span><span id="31958329-4828-472f-a266-c6263e5a6193" class="GINGER_SOFTWARE_mark">dwca</span></span></span>-teste3<span><span><span id="38fc3ba4-5f5d-4f79-ba54-608888ee85fd" class="GINGER_SOFTWARE_mark">.</span></span></span>zip</b></div>
<div>2014-04-28 01:56:04,683 INFO<span><span><span id="004b637d-aaee-4cfe-9e1b-6d5845911b5e" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="f7237b49-bec7-4b2f-96fa-85538cbc87cd" class="GINGER_SOFTWARE_mark">ConfigModule</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 id="89e1dfe7-f8dc-479c-bfeb-490e631114c5" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="eddab447-77ab-40a5-883f-739299981410" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span>]
- Initialise SOLR</div>
<div>2014-04-28 01:56:04,951 INFO<span><span><span id="5c210b6b-8d42-4f32-8deb-1ea0d5d68b43" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="c4bee0cd-1ccf-48f4-9294-431be010cc91" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span>]
- <span><span><span id="c37fba09-3d5a-46fa-b68f-ff79927ffd14" class="GINGER_SOFTWARE_mark">Initialise</span></span></span> name matching indexes</div>
<div>2014-04-28 01:56:05,437 INFO<span><span><span id="b2e2d0d3-a9f7-41ac-a172-be7081989371" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="8e8de775-ff2b-4c15-b1e8-03920e627d57" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span>]
- Initialise persistence manager</div>
<div>2014-04-28 01:56:05,438 INFO<span><span><span id="a454740d-ab43-4a57-9c66-9648aa0725b7" class="GINGER_SOFTWARE_mark"> :</span></span></span> [<span><span><span id="0609e9b4-0baa-49ac-b353-769565edfa22" class="GINGER_SOFTWARE_mark">ConfigModule</span></span></span>]
- Configure complete</div>
<div>Loading archive<span><span><span id="b8c27fd6-4bb1-4f92-be89-9cfff7d023c4" class="GINGER_SOFTWARE_mark"> .</span></span></span>/<span><span><span id="9cf7bbd9-d6b2-4e56-b599-fb06837f93c8" class="GINGER_SOFTWARE_mark">dwca</span></span></span>-teste3<span><span><span id="72cb13f8-acaf-4181-9788-03bb99bf29e3" class="GINGER_SOFTWARE_mark">.</span></span></span>zip
for resource dr7 with unique terms List<span><span><span id="18e4a3e5-5b9f-4e03-beea-63384c4b7817" class="GINGER_SOFTWARE_mark">(</span></span></span><span><span><span id="8b7baa58-4aa6-477f-85b0-afe9000c68f3" class="GINGER_SOFTWARE_mark">dwc</span></span></span><span><span><span id="91958ced-4ffe-4f2c-ad7c-97dd5498a2a4" class="GINGER_SOFTWARE_mark">:</span></span></span><span><span><span id="3b2d6820-fc6c-49cc-a2c3-d10b2f81952c" class="GINGER_SOFTWARE_mark">occurrenceID</span></span></span>)
stripping spaces false incremental false testing <span><span><span id="ddc98534-3587-4fa4-b3f6-6b99713148c5" class="GINGER_SOFTWARE_mark">false</span></span></span></div>
<div><b>Exception in thread "main" org<span><span><span id="fbec6da6-29c8-48f8-90ec-34584b1e2478" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="926f9a52-f865-452c-86c2-7009c6f7e2f7" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="be8b9c28-d82b-4056-8515-e2c4522e4a27" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="972283a6-5cd1-44be-9048-6cf30c42a863" class="GINGER_SOFTWARE_mark">dwc</span></span></span><span><span><span id="eeafe3d1-ae70-4652-8382-36667b274df1" class="GINGER_SOFTWARE_mark">.</span></span></span>text<span><span><span id="8a27f1cf-a57d-4868-9eb1-cd2336fa14bc" class="GINGER_SOFTWARE_mark">.</span></span></span>UnkownDelimitersException:
Unable to detect field delimiter</b></div>
<div> <span><span><span id="2a6b1b11-e1ec-40ea-8a67-df4c66bc92ab" class="GINGER_SOFTWARE_mark">at</span></span></span> org<span><span><span id="f6bfec6d-4a50-49bc-a7f6-8077bae99358" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="7bf2f16d-7a18-4007-bf1a-5baa1ee2a77b" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="80f710fd-3a1e-4809-83d4-c9f1484b146b" class="GINGER_SOFTWARE_mark">.</span></span></span>file<span><span><span id="5924289a-0428-4bdc-b1b5-b210e7a82b33" class="GINGER_SOFTWARE_mark">.</span></span></span>CSVReaderFactory<span><span><span id="4512bcda-1f58-4654-9b57-7db767b6636c" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="23e86c28-855a-48c2-9d76-b02bd12bd73b" class="GINGER_SOFTWARE_mark">buildArchiveFile</span></span></span><span><span><span id="701c4043-0b37-4a0e-bb88-9cc48747b491" class="GINGER_SOFTWARE_mark">(</span></span></span>CSVReaderFactory.java<span><span><span id="32988908-32e5-4ce3-b5bb-a559473b087a" class="GINGER_SOFTWARE_mark">:</span></span></span>129)</div>
<div> <span><span><span id="13730837-d312-406e-bd6e-f967acd92c82" class="GINGER_SOFTWARE_mark">at</span></span></span> org<span><span><span id="90c2db7d-a346-47b4-902c-fcbe52cd3445" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="e2bd7f2e-7eeb-4829-bc36-a96713902514" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="75b629fe-a71a-4aa4-aaf7-644589fe640a" class="GINGER_SOFTWARE_mark">.</span></span></span>file<span><span><span id="4b12ad82-eef8-4718-8a41-f43dd53b7d96" class="GINGER_SOFTWARE_mark">.</span></span></span>CSVReaderFactory<span><span><span id="23729dd1-bd4c-4cec-be8d-ac83c087d0f4" class="GINGER_SOFTWARE_mark">.</span></span></span>build<span><span><span id="2ccea8fb-4d2c-47ec-ad34-7e54958ab8ff" class="GINGER_SOFTWARE_mark">(</span></span></span>CSVReaderFactory.java<span><span><span id="907689f5-f34f-4413-b572-c831b495a019" class="GINGER_SOFTWARE_mark">:</span></span></span>46)</div>
<div> <span><span><span id="f93d4c6c-6c32-4217-8212-e110acd8572f" class="GINGER_SOFTWARE_mark">at</span></span></span> org<span><span><span id="fa44eb40-f50f-43ec-8fae-8b592cd71ac0" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="eb6ecbaf-1f05-4600-8c9c-4ae751cdc88d" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="2198a539-b0fc-4005-9fea-46574f87f6d0" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="b65269cc-c0ba-4cb1-8dae-961d90eed5d5" class="GINGER_SOFTWARE_mark">dwc</span></span></span><span><span><span id="bfb7db9b-8cc9-440c-a3fb-3600a74fdd9d" class="GINGER_SOFTWARE_mark">.</span></span></span>text<span><span><span id="68762f0c-f746-4302-9844-102db4cf435c" class="GINGER_SOFTWARE_mark">.</span></span></span>ArchiveFactory<span><span><span id="f5bcd9ad-c263-459b-969b-12cb49852edd" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="dda25edb-e772-4929-bd08-e5b0223ffe46" class="GINGER_SOFTWARE_mark">readFileHeaders</span></span></span><span><span><span id="3f78974c-5bf6-41b5-8c6d-48f0d5e53c57" class="GINGER_SOFTWARE_mark">(</span></span></span>ArchiveFactory.java<span><span><span id="d2d6e3fc-7933-44f7-8857-42f2b3317374" class="GINGER_SOFTWARE_mark">:</span></span></span>344)</div>
<div> <span><span><span id="56294dae-05b6-4c34-b380-f38534cd7beb" class="GINGER_SOFTWARE_mark">at</span></span></span> org<span><span><span id="d8d22167-891c-4f47-8702-7d44bc54c77b" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="a58365c6-8a70-4af0-9739-697d1d55b8c0" class="GINGER_SOFTWARE_mark">gbif</span></span></span><span><span><span id="f105219b-3588-444d-b159-6bfe26856be2" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="220d001c-29ca-4e61-8326-2a2680f8aa9d" class="GINGER_SOFTWARE_mark">dwc</span></span></span><span><span><span id="e0defce1-3e23-4861-a531-a9ffb7e9501c" class="GINGER_SOFTWARE_mark">.</span></span></span>text<span><span><span id="583ea3ea-cb2a-4b3e-aee3-44215765becd" class="GINGER_SOFTWARE_mark">.</span></span></span>ArchiveFactory<span><span><span id="046646c1-d6e0-4976-ae6c-b6cfb92a567e" class="GINGER_SOFTWARE_mark">.</span></span></span><span><span><span id="7b4c1c27-8b4a-4686-a38f-cc034d26b52f" class="GINGER_SOFTWARE_mark">openArchive</span></span></span><span><span><span id="8c33623d-ddca-4381-86a5-d665ef1f32a4" class="GINGER_SOFTWARE_mark">(</span></span></span>ArchiveFactory.java<span><span><span id="5cf4b87d-cd04-4e44-92e3-4221acec700e" class="GINGER_SOFTWARE_mark">:</span></span></span>289)</div>
<div> <span><span><span id="b6f1f698-fbf1-4714-9f90-c7487f4d4797" class="GINGER_SOFTWARE_mark">at</span></span></span> au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129)</div>
<div> <span><span><span id="94edf239-71ac-4f18-8fad-16e88e3b0c9a" class="GINGER_SOFTWARE_mark">at</span></span></span> au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106)</div>
<div> <span><span><span id="10dcb023-b2e1-4401-9335-b31f5064cdc0" class="GINGER_SOFTWARE_mark">at</span></span></span> au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52)</div>
<div> <span><span><span id="197917c6-8db1-4cf8-b570-6298d36fb393" class="GINGER_SOFTWARE_mark">at</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 id="5bfd1ce4-2da7-4b4d-b393-18fb1c4d945c" 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="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>
</div>
<div><br>
</div>
</div>
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</div>
</blockquote>
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</div>
</span></div>
</blockquote>
</div>
</div>
</div>
<span class=""><font color="#888888"><br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>Daniel Lins da Silva<br>
(<span id="04892894-0f74-40cf-a630-4db67e9fc507" class="GINGER_SOFTWARE_mark">Cel</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>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>Daniel Lins da Silva<br>
(<span id="c7d33527-2b40-4693-a709-9ae250be5466" class="GINGER_SOFTWARE_mark">Cel</span>) 11 6144-4050</div>
<div><a href="mailto:daniel.lins@gmail.com" target="_blank">daniel.lins@gmail.com</a><br>
</div>
</div>
</div>
</div>
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