Processing Data Workflow

1. Visit Site & Download Data with Toughbook
   1. data should go in ~/Dropbox/logger_data/$YEAR/$SITE/
   2. general naming convention for data files is: $SITE_$TABLE-$YEAR_$MONTH_DAY.dat
2. Back in town, put toughbook online so it can be mirrored by other computers
3. Back to office, copy this data from dropbox to /var/site/$AREA/$SITE/raw or similar
4. Most processing scripts are located in /var/site/bin/ with name like process_$SITE.sh
5. to this script add lines in each appropriate section so that datapro can process this new data
6. In the initial cut here (I'm just starting to do this 10/2018) I have two bash functions in the script. They're related. 1) is delete all the processed data in /var/site/$AREA/$SITE/outputs and 2) is apply the manual QA. In the bash script, I comment the calls to do those two things first run so that the processing is quicker. So, edit the bash file to comment the two function calls, too.
7. next, run the bash script.
8. once done the data will appear here: /var/site/$AREA/$SITE/outputs/. I have a web page that can be used for visualizations. /var/site/$AREA/$SITE/index.html after the automated processing has fixed everything then I review this page to catch things it misses (for instance, animal damage knocking a radiometer off level, other oddities where the data appears right but isn't quite.)
9. Any manual corrections go in an excel spreadsheet. /var/site/$AREA/$SITE/qc/$SENSORNAME_fixes.xlsx
10. there should be a line in the process_$SITE.sh subroutine for manual fixes for this file (most don't have this line until there is manually correcting to do).
11. After manual corrections are complete and script is updated, re-run /var/site/bin/process_$SITE.sh with everything uncommented so that final dataset is created from scratch and manual edits are applied.
12. upload the final product from local computer to main server / or data archive etc