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Large quantities of ecological and environmental data are increasingly available thanks to initiatives sponsoring the collection of large-scale data and efforts to increase the publication of already collected datasets. As a result, progress in ecology is increasingly limited by the speed at which we can organize and analyze data. To help improve ecologists' ability to quickly access and analyze data we have been developing software that designs database structures for ecological datasets and then downloads the data, pre-processes it, and installs it into major database management systems (at the moment we support MySQL, PostreSQL, SQLite, and Microsoft Access).

Once the Database Toolkit has loaded the data into the database it is easy to connect to the database using standard tools (e.g., MS Access, Filemaker, etc.).These Database Toolkits can download and install small datasets in seconds and large datasets in minutes. The programs also cleanup known issues with the datasets and automatically restructure them into a format appropriate for standard database management systems. 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.

 

Downloads

The Database Toolkit binaries and source are released under the MIT license.

The Database Toolkit is currently in beta release, so we're still in the process of finding and correcting errors. These files may change frequently before the final release of version 1.0. This beta release was last updated on September 29, 2010 at 4:00 PM.

File NameDescription
dbtk.exe Windows executable
python-dbtk_0.1-1_all.deb Debian package (Linux)
dbtk-src.tar.gz Source package

 

Documentation

 

Acknowedgments

The current implementation was written by Ben Morris with help from Ethan White. Glenda Yenni provided valuable assistance by manually importing a number of the databases; thus allowing the development of automated tests for the system. This work was funded by the National Science Foundation as part of a CAREER award to Ethan White.

 

License

Copyright (c) 2010 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.