Loads Trait data in CSV files to BETYdb.
Below is a sample command line that shows how the field mosaic 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/betydb-csvupload:2.0 --working_space "/mnt" "/mnt/ir_fullfield_L2_ua-mac_2018-06-03_stereovis_ir_sensors_partialplots_sorghum6_sun_flir_eastedge_mn_meantemp_bety.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/betydb-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.
runindicates we want to run an image--rmautomatically delete the image instance after it's run--mount "src=/home/test,target=/mnt,type=bind"mounts the/home/testfolder to the/mntfolder of the running image-e "BETYDB_URL=<BETYdb URL>"specifies the URL of the BETYdb instance to load data to-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/mnt/ir_fullfield_L2_ua-mac_2018-06-03_stereovis_ir_sensors_partialplots_sorghum6_sun_flir_eastedge_mn_meantemp_bety.csvis the name CSV file to upload