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Finding data is one thing. Getting it ready to use is another.

The EcoData Retriever does all the work so that you can focus on doing science.

Most ecological datasets do not adhere to any agreed-upon standards in format, data structure or method of access. As a result acquiring and utilizing available datasets can be a time consuming and error prone process. The EcoData Retriever automates the tasks of finding, downloading, and cleaning up ecological data files, and then stores them in a local database. The automation of this process reduces the time for a user to get most large datasets up and running by hours, and in some cases days. Small datasets can be downloaded and installed in seconds and large datasets in minutes. The program also cleans up known issues with the datasets and automatically restructures them into standard formats before inserting the data into your choice of database management systems (Microsoft Access, MySQL, PostgreSQL, and SQLite, on Windows, Mac and Linux).

Downloads

The EcoData Retriever binaries and source are released under the MIT license.

File Name Description Version Date Updated
retriever.exe Windows executable 1.4 05/30/2012
python-retriever_1.4-1_all.deb Debian package (Linux) 1.4 05/30/2012
mac-retriever-1-4.zip Mac bundle
 1.4 Alpha* 05/30/2012
retriever-src.tar.gz Source package 1.4 05/30/2012

*We don't use Macs, so we have very limited abilities to test the Mac bundle. Therefore the Mac bundle is currently in Alpha and we have had reports of failures. Please let us know how it works for you. If the bundle does not work building from source with the required dependencies should.

You can also clone the GitHub repository if you want to work with the latest (unstable) version.

Documentation

 

Report an issue

We are currently in the beta testing phase of development and would greatly appreciate any and all feedback, tests of various imports, bug reports, etc. You can either submit an issue at Github or email us directly. 

 

Acknowledgments

The EcoData Retriever was written by Ben Morris with help from Ethan White. This work was funded by the National Science Foundation as part of a CAREER award to Ethan White. Contributors include Glenda Yenni (testing) and Kate Thibault (dataset scripts).

 

Publications using the EcoData Retriever

White, E.P., K.M. Thibault, and X. Xiao. 2012. Characterizing species-abundance distributions across taxa and ecosystems using a simple maximum entropy model. Ecology. http://dx.doi.org/10.1890/11-2177.1


License

Copyright (c) 2011 Weecology

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Comments

Submitted by Allen Hurlbert on Tue, 2010-10-05 06:41

I'm unclear on what I should be specifying for Connection Info. I specified MS Access early on, so here it appears to be wanting an Access database file. This window could use a sentence of explanation. I get an error just using the default filename : "There was an error with your databae connection .... Not a valid filename."

Submitted by Allen Hurlbert on Tue, 2010-11-16 15:39

Ok, so I take pride in being your quintessential idiot end user. For idiots like me, I would have to say that it is still unclear how exactly the Toolkit is supposed to work. It is providing me with a way to connect to the datasets that you are hosting? It is a way of downloading and pre-processing the data and storing a copy on my own machine? I guess it's unclear to me what I'm supposed to have done prior to running dbtk.exe. I created a blank Access database. Does it matter what the "Data file directory" is? This is just where raw data files are going to get stored right? Is there some specific directory structure I'm supposed to be using here? I tried leaving it as the default, as well as creating some new folder. At any rate, after specifying the directory and connection info, clicking on any of the datasets results in a "There was an error with your database connection."

Submitted by Ethan White on Fri, 2010-11-19 06:39

Thanks for the feedback Allen (FYI I still don't have notifications set up for this part of the site so you might want to ping me via email if you'd like a quick response). I think Ben just rolled out an update that at least instructs the user to create the MS Access file before proceeding, but we've clearly got a long way to go in this area.

To answer your questions briefly:

  1. The idea of the system is that it is storing a copy of all of the data one your machine. This circumvents all of the complexities related to hosting other people's data.
  2. You are right about the "Data file directory" and the default should work, but I'm wondering if this is something that should be removed or at least hidden in an advanced tab to avoid confusion since most users won't care.

You shouldn't be getting an error if you created a blank Access database and then selected that file when asked for your connection information. Can you give us a detailed run down of the steps you took so that we can track down the problem. Thanks.