Data Pipeline

Data flow schematic

Micromet Data Flow (currently for BB1, BB2, DSM, and RBM)
Note: Manitoba sites have SmartFlux stream only

Drive/Folder structure on vinimet

  • P:\Sites\Site (data as received from the sites)

                      \5min (for BB only)
  • P:\Database (everything in read_bor format)

                           \Met (straight from CRBasic -> read_bor)
                               \Clean (First stage clean)
                           \Flux (from EddyPro summary, site files -> read_bor & then overwrite with EddyPro recalculated output) 
                               \Clean (First stage clean)
                                 \ThirdStage_REddyProc_RF_Fast (simple uncertainty analysis)
                                 \ThirdStage_REddyProc_RF_Full (full uncertainty analysis)
  • P:\Micromet_web (note that this mirrors what’s on host

                        \data (html & javascript for site level web plotting)
                        \webdata\resources\csv (csv files for web plotting)
  • Google drive contains:

    • Pictures (to remove and host on google photos)
    • Documents

Data stream notes

The data processing is run from LoggerNet Task manager through batch files stored under c:\UBC_Flux\BiometFTPsite. The batch files are named: Site_automatic_processing.bat. The generic Matlab scripts that’s called from these batch files is: run_BB_db_update([],{‘Site’},0)

More Details

  • MET Files

    • Every 4 hrs (e.g., BB1 4:20, BB2 4:10) Loggernet Task Master downloads MET data to P:\Sites\Site\Met\Site_MET.dat (or Site_biomet.dat)

    Note Site is used generically to refer to each site (e.g., BB, BB2, DSM, RBM, Hogg, Young)

  • Once per day 1:10 am

    • ‘Rename files for all sites’ - Called from Loggernet Task Master
      • Renames Site_MET.dat to Site_MET.yyyyddd
      • -nosplash /r “renam_csi_dat_files”('P:Sites\Site\Met');…for each site; exit;”
    • Site_Process_CSI_to_database - Called from Loggernet Task Master
      • -nosplash -minimize /r “run_BB_db_update([],{‘Site’});”

          function run_BB_db_update(yearln)
            dv = datevec(now);
            arg_defualt('yearln', dv(1));
            sites = {'Site'};
            db_update_BB_site(yearln, sites);
    • db_update_BB_site
      • Update Site matlab database with new logger files to P:\Database\yyyy\Site\Met
      • Call C:\UBC_PC_Setup\PC_specific\BB_webupdate to create .csv files used by webplots -> `P:_web
      • Call C:\Ubc_flux\BiometFTPsite\BB_Web_Update.bat to move csv files to webserver
  • Location of data

    • P: - local drive on vinimet
    • P:\Micromet_web\www\webdata\resources\csv - location of CSV files
    • P:\Micromet_web\www\data - local versions of js, html files
    • P:\Sites\Sites - raw data

Web-plotting pipeline

First, go from the bottom of the chart in the first page upwards, find out which step stopped working then use the followiwng instructions to troubleshoot.

EC Data

  1. SmartFlux files (*_EP-Summary.txt) arrive in the folders as below: \\\Projects\Sites\BB\Flux \\\Projects\Sites\BB2\Flux

insert image

  • Troubleshooting for Step 1:
    • If there is NO recent data files (.zip or .txt) at all, then:

      • Check if you can still connect to LI-7200 to determine if it is an Internet issue or not.
      • Check if the LoggerNet task for data downloads failed. When all tasks are executed properly, the status of the tasks should be shown like this:

      insert image

      • Check if the SmartFlux system at site skips processing or not by using WinSCP connecting to it (e.g., BB_site or BB2_site). The second figure below shows the BB2 SmartFlux have skipped processing of Feb. 1 (there is no summary file for that day):

      insert images

  1. If SmartFlux files arrive, the task “XX_automatic_processing” (as shown in the figure above) that runs Matlab program will process all data (CSI and SmartFlux) and update the web files too.

    • Troubleshooting for Step 2:
      • If you suspect that this task failed, then:
        • Check the dates of the last updated web csv files (\\VINIMET.GEOG.UBC.CA\Micromet_web\www\webdata\resources\csv).
        • Check a few flux-related csv files to see if the last datestamps are less than 6 hours old.
        • If the files are NOT up-to-date, manually rerun the Matlab program by using run_BB_db_update([]{'BB2},0)
      • If you confirm the task is working fine or you’ve re-run the Matlab program, then:
        • Check if those files were uploaded to the web server by starting WinSCP to connect to ‘’ and see if the files are there.

Met Data

Data from dataloggers goes to \\\Projects\Sites\BB\Met\ or \\\Projects\Sites\BB2\Met\.

  • Troubleshooting:
    1. Check if the files have arrived or not.
    2. Check the LoggerNet task for data downloads.
    3. Check connection to the logger
    4. Check the data of the last updates Biomet database files (\\VINIMET.GEOG.UBC.CA\Database)
    5. Check a few MET-related csv files to see if the last datestamps are less than 6 hours old.
    6. Manually re-run the task in Matlab by using run_BB_db_update([]{'BB2},0).
    7. Check if those csv files were uploaded to the web server.

Continue adding info from here

Other Documentation & Tasks

The following documents in the General procedures, settings and protocols folder in Google Drive may also be of use:

  • Updating webplots → Micromet web plotting.docx
  • Documents for dealing with full internal memory for SmartFlux → Note_SmartFlux internal memory_ssh connection.docx & Note_SmartFlux internal memory_updater.docx
  • 7200 lab calibration → Note_LI-7200 Lab calibration procedure.docx
  • Gas tank calibration → Report_Gas tank calibration.docx

NOTE: Note that the troubleshooting reports folder contains documentation on troubleshooting that is relevant to all sites.

Creating a local copy of the database

To create a local copy of the Micromet Lab database or create your own database following the Micromet Lab database structure, following the instructions provided here