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Transformer: GeoStreams CSV file upload

Loads Trait data in CSV files to GeoStreams through the Clowder API.

Sample Docker Command Line

Below is a sample command line that shows how the GeoStreams CSV file upload Docker image could be run. An explanation of the command line options used follows. Be sure to read up on the docker run command line for more information.

The files used in this sample command line can be found on Google Drive.

docker run --rm --mount "src=/home/test,target=/mnt,type=bind" -e "BETYDB_URL=<BETYdb URL>" -e "BETYDB_KEY=<BETYdb Key>" agpipeline/geostream_csvupload:2.0 --working_space /mnt --clowder_url "<Clowder URL>" --clowder_key "<Clowder Key>"  /mnt/rgb_fullfield_L2_ua-mac_2018-06-28_stereovis_ir_sensors_partialplots_sorghum6_sun_flir_eastedge_mn_2_mask_canopycover_geo.csv"

This example command line assumes the source files are located in the /home/test folder of the local machine. The name of the image to run is agpipeline/geostream_csvupload:2.0.

We are using the same folder for the source files and the output files. By using multiple --mount options, the source and output files can be separated.

Docker commands
Everything between 'docker' and the name of the image are docker commands.

  • run indicates we want to run an image
  • --rm automatically delete the image instance after it's run
  • --mount "src=/home/test,target=/mnt,type=bind" mounts the /home/test folder to the /mnt folder of the running image
  • -e "BETYDB_URL=<BETYdb URL>" specifies the URL of the BETYdb instance from which to fetch site (plot-level) data
  • -e "BETYDB_KEY=<BETYdb Key>" specifies the permission key used to access the BETYdb instance

We mount the /home/test folder to the running image to make files available to the software in the image.

Image's commands
The command line parameters after the image name are passed to the software inside the image. Note that the paths provided are relative to the running image (see the --mount option specified above).

  • --working_space "/mnt" specifies the folder to use as a workspace
  • --clowder_url "<Clowder URL>" the URL of the Clowder instance to upload data to
  • --clowder_key "<Clowder Key>" the key to use when accessing the Clowder instance
  • /mnt/rgb_fullfield_L2_ua-mac_2018-06-28_stereovis_ir_sensors_partialplots_sorghum6_sun_flir_eastedge_mn_2_mask_canopycover_geo.csv is the name CSV file to upload