Test out SciF image on Cereus

[Chris-Schnaufer]

Task to do Test SciF container on Cereus by processing data

Reason Show that the SciF container works on the Cereus

Result Determine confidence level regarding SciF container working on Cereus

Apps to try

• [ ] Soil mask (either traditional soilmask or ratio_soilmask app)
• [ ] Plot clipping
• [ ] Find files app (locates plot-clipped images and writes JSON file)
• [ ] Canopy Cover or Greenness Indices calculation

[Chris-Schnaufer]

Sample data set can be found at: https://de.cyverse.org/dl/d/3C8A23C0-F77A-4598-ADC4-874EB265F9B0/scif_test_data.tar.gz

Sample docker command lines (with a docker image named chrisatua/development:drone_makeflow), the input folder always contains the input files, output is places in the output folder, and see below for the contents of the chris-jx-args.json file (change as needed):

• BETYdb2GeoJson: docker run --rm -v ${PWD}/output:/output -v ${PWD}/chris-jx-args.json:/scif/apps/src/jx-args.json chrisatua/development:drone_makeflow run betydb2geojson
• shp2GeoJson: docker run --rm -v ${PWD}/inputs:/input -v ${PWD}/output:/output -v ${PWD}/chris-jx-args.json:/scif/apps/src/jx-args.json chrisatua/development:drone_makeflow run shp2geojson
• soilmask: docker run --rm -v ${PWD}/inputs:/input -v ${PWD}/output:/output -v ${PWD}/chris-jx-args.json:/scif/apps/src/jx-args.json chrisatua/development:drone_makeflow run soilmask
• plotclip: docker run --rm -v ${PWD}/inputs:/input -v ${PWD}/output:/output -v ${PWD}/chris-jx-args.json:/scif/apps/src/jx-args.json chrisatua/development:drone_makeflow run plotclip
• find_files2json: docker run --rm -v ${PWD}/inputs:/input -v ${PWD}/output:/output -v ${PWD}/chris-jx-args.json:/scif/apps/src/jx-args.json chrisatua/development:drone_makeflow run find_files2json
• canopycover: docker run --rm -v ${PWD}/inputs:/input -v ${PWD}/output:/output -v ${PWD}/chris-jx-args.json:/scif/apps/src/jx-args.json -v ${PWD}/output/canopy_cover_files.json:/scif/apps/src/canopy_cover_files.json chrisatua/development:drone_makeflow run canopycover
• greenness: docker run --rm -v ${PWD}/inputs:/input -v ${PWD}/output:/output -v ${PWD}/chris-jx-args.json:/scif/apps/src/jx-args.json -v ${PWD}/output/canopy_cover_files.json:/scif/apps/src/greenness-indices_files.json chrisatua/development:drone_makeflow run greenness-indices
• mergecsv: docker run --rm -v ${PWD}/output:/input -v ${PWD}/output:/output -v ${PWD}/chris-jx-args.json:/scif/apps/src/jx-args.json chrisatua/development:drone_makeflow run merge_csv

chris-jx-args.json

{
  "BETYDB_URL": "https://terraref.ncsa.illinois.edu/bety",
  "PLOT_SHAPEFILE": "/input/plot_shapes.shp",
  "PLOT_GEOMETRY_FILE": "/output/plots.geojson",
  "SOILMASK_SOURCE_FILE": "/input/orthomosaic.tif",
  "SOILMASK_MASK_FILE": "orthomosaicmask.tif",
  "SOILMASK_WORKING_FOLDER": "/output",
  "SOILMASK_OPTIONS": "",
  "SOILMASK_RATIO_SOURCE_FILE": "/input/orthomosaic.tif",
  "SOILMASK_RATIO_MASK_FILE": "orthomosaicmask.tif",
  "SOILMASK_RATIO_WORKING_FOLDER": "/output",
  "SOILMASK_RATIO_OPTIONS": "--ratio 1.0",
  "PLOTCLIP_SOURCE_FILE": "/output/orthomosaicmask.tif",
  "PLOTCLIP_PLOTGEOMETRY_FILE": "/output/plots.geojson",
  "PLOTCLIP_WORKING_FOLDER": "/output",
  "PLOTCLIP_OPTIONS": "",
  "FILES2JSON_SEARCH_NAME": "orthomosaicmask.tif",
  "FILES2JSON_SEARCH_FOLDER": "/output",
  "FILES2JSON_JSON_FILE": "/output/canopy_cover_files.json",
  "CANOPYCOVER_OPTIONS": "",
  "GREENNESS_INDICES_OPTIONS": "",
  "MERGECSV_SOURCE": "/input",
  "MERGECSV_TARGET": "/output",
  "MERGECSV_OPTIONS": " --ignore-dirs logs,and,others "
}

[jvanderleeuw]

Testing worked correctly/exit codes were all 0 and the tests were able to run sequentially