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Merge pull request #74 from AgPipeline/develop
Fixing up Actions for new ubuntu version
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| Original file line number | Diff line number | Diff line change |
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| %appinstall canopycover | ||
| # Download canopycover code. In the future use pip/conda install. | ||
| wget -O canopycover.tar.gz https://github.com/AgPipeline/transformer-canopycover/archive/v1.8.tar.gz | ||
| tar xvf canopycover.tar.gz | ||
| mv transformer-canopycover-1.8 src | ||
| echo "Removing unneeded files" | ||
| rm -rf --verbose src/test_data src/tests src/.github canopycover.tar.gz | ||
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| # Install Makeflow and other dependencies | ||
| python3.8 -m venv --system-site-packages .venv | ||
| .venv/bin/python3 -m pip install --upgrade --no-cache-dir pip | ||
| .venv/bin/python3 -m pip install --upgrade --no-cache-dir -r "${PWD}/src/requirements.txt" | ||
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| # Add example Docker command to SCIF app help section | ||
| if [ -n $DOCKER_IMAGE ]; then | ||
| echo "\n\nExample Docker command: docker run $DOCKER_IMAGE run canopycover\n" >> "${PWD}/scif/runscript.help" | ||
| fi | ||
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| # Generate remainder of SCIF app help section by running main script | ||
| .venv/bin/python3 src/canopycover.py --help >> "${PWD}/scif/runscript.help" | ||
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| %apprun canopycover | ||
| /cctools/bin/makeflow \ | ||
| --jx \ | ||
| --jx-args="/scif/apps/src/jx-args.json" \ | ||
| --jx-args="/scif/apps/src/canopy_cover_files.json" \ | ||
| --log-verbose \ | ||
| --retry-count=1 \ | ||
| --change-directory="${SCIF_APPDATA}" \ | ||
| --makeflow-log="${SCIF_APPDATA}/workflow.jx.makeflowlog" \ | ||
| --batch-log="${SCIF_APPDATA}/workflow.jx.batchlog" \ | ||
| ${1} \ | ||
| "/scif/apps/src/canopycover_workflow.jx" | ||
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| %apphelp canopycover | ||
| This app provides an entrypoint to the canopycover tool |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| %appinstall git_rgb_plot | ||
| # Install Makeflow and other dependencies | ||
| python3.8 -m venv --system-site-packages .venv | ||
| .venv/bin/python3 -m pip install --upgrade --no-cache-dir pip | ||
| .venv/bin/python3 -m pip install --upgrade --no-cache-dir opencv-contrib-python-headless agpypeline | ||
|
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| # Add example Docker command to SCIF app help section | ||
| if [ -n $DOCKER_IMAGE ]; then | ||
| echo "\n\nExample Docker command: docker run $DOCKER_IMAGE run git\n" >> "${PWD}/scif/runscript.help" | ||
| fi | ||
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| # Generate remainder of SCIF app help section by running main script | ||
| .venv/bin/python3 /scif/apps/src/git_algo_rgb_plot.py --help >> "${PWD}/scif/runscript.help" | ||
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| %apprun git_rgb_plot | ||
| /cctools/bin/makeflow \ | ||
| --jx \ | ||
| --jx-args="/scif/apps/src/jx-args.json" \ | ||
| --jx-args="/scif/apps/src/git_rgb_plot_files.json" \ | ||
| --log-verbose \ | ||
| --retry-count=1 \ | ||
| --change-directory="${SCIF_APPDATA}" \ | ||
| --makeflow-log="${SCIF_APPDATA}/workflow.jx.makeflowlog" \ | ||
| --batch-log="${SCIF_APPDATA}/workflow.jx.batchlog" \ | ||
| ${1} \ | ||
| "/scif/apps/src/git_rgb_plot_workflow.jx" | ||
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| %apphelp git_rgb_plot | ||
| This app provides an entrypoint to the git tool |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| %appinstall greenness-indices | ||
| # Install Makeflow and other dependencies | ||
| python3.8 -m venv --system-site-packages .venv | ||
| .venv/bin/python3 -m pip install --upgrade --no-cache-dir pip | ||
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| # Download plot-base-rgb code | ||
| wget -O plot_base_rgb.tar.gz https://github.com/AgPipeline/plot-base-rgb/archive/v1.10.tar.gz | ||
| tar xvf plot_base_rgb.tar.gz | ||
| mv plot-base-rgb-1.10 src | ||
| .venv/bin/python3 -m pip install --upgrade --no-cache-dir -r "${PWD}/src/requirements.txt" | ||
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| # Download greenness-indices code. In the future use pip/conda install. | ||
| wget -O greenness_indices.tar.gz https://github.com/AgPipeline/transformer-rgb-indices/archive/v1.4.tar.gz | ||
| tar xvf greenness_indices.tar.gz | ||
| cp -r transformer-rgb-indices-1.4/* src/ | ||
| rm -r transformer-rgb-indices-1.4 | ||
| .venv/bin/python3 -m pip install --upgrade --no-cache-dir -r "${PWD}/src/requirements.txt" | ||
| echo "Removing unneeded files" | ||
| rm -rf --verbose src/test_data src/tests src/.github plot_base_rgb.tar.gz greenness_indices.tar.gz | ||
|
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| # Add example Docker command to SCIF app help section | ||
| if [ -n $DOCKER_IMAGE ]; then | ||
| echo "\n\nExample Docker command: docker run $DOCKER_IMAGE run greenness-indices\n" >> "${PWD}/scif/runscript.help" | ||
| fi | ||
|
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||
| # Generate remainder of SCIF app help section by running main script | ||
| .venv/bin/python3 src/transformer.py --help >> "${PWD}/scif/runscript.help" | ||
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| %apprun greenness-indices | ||
| /cctools/bin/makeflow \ | ||
| --jx \ | ||
| --jx-args="/scif/apps/src/jx-args.json" \ | ||
| --jx-args="/scif/apps/src/greenness-indices_files.json" \ | ||
| --log-verbose \ | ||
| --retry-count=1 \ | ||
| --change-directory="${SCIF_APPDATA}" \ | ||
| --makeflow-log="${SCIF_APPDATA}/workflow.jx.makeflowlog" \ | ||
| --batch-log="${SCIF_APPDATA}/workflow.jx.batchlog" \ | ||
| ${1} \ | ||
| "/scif/apps/src/greenness-indices_workflow.jx" | ||
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| %apphelp greenness-indices | ||
| This app provides an entrypoint to the greenness-indices tool |
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| %appinstall betydb2geojson | ||
| # Install dependencies | ||
| python3.8 -m venv --system-site-packages .venv | ||
| .venv/bin/python3 -m pip install --upgrade --no-cache-dir pip | ||
| .venv/bin/python3 -m pip install --upgrade --no-cache-dir requests pygdal==3.4.1.* | ||
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| %apprun betydb2geojson | ||
| /cctools/bin/makeflow \ | ||
| --jx \ | ||
| --jx-args="/scif/apps/src/jx-args.json" \ | ||
| --log-verbose \ | ||
| --retry-count=1 \ | ||
| --change-directory="${SCIF_APPDATA}" \ | ||
| --makeflow-log="${SCIF_APPDATA}/workflow.jx.makeflowlog" \ | ||
| --batch-log="${SCIF_APPDATA}/workflow.jx.batchlog" \ | ||
| ${1} \ | ||
| "/scif/apps/src/betydb2geojson_workflow.jx" | ||
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| %apphelp betydb2geojson | ||
| This app provides a conversion from BETYdb site data to GeoJSON plot geometries. | ||
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| Expected keys in the "jx-args.json" file: | ||
| BETYDB_URL - the value is the URL of the BETYdb instance to get plot geometries from | ||
| PLOT_SHAPEFILE - the path to save the GeoJSON to | ||
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| Sample command: | ||
| scif run betydb2geojson | ||
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| See also: | ||
| https://github.com/AgPipeline/drone-makeflow/blob/master/README.md | ||
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| %appinstall shp2geojson | ||
| # Install dependencies | ||
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| %apprun shp2geojson | ||
| /cctools/bin/makeflow \ | ||
| --jx \ | ||
| --jx-args="/scif/apps/src/jx-args.json" \ | ||
| --log-verbose \ | ||
| --retry-count=1 \ | ||
| --change-directory="${SCIF_APPDATA}" \ | ||
| --makeflow-log="${SCIF_APPDATA}/workflow.jx.makeflowlog" \ | ||
| --batch-log="${SCIF_APPDATA}/workflow.jx.batchlog" \ | ||
| ${1} \ | ||
| "/scif/apps/src/shp2geojson_workflow.jx" | ||
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| %apphelp shp2geojson | ||
| This app provides a conversion from a shapefile to GeoJSON plot geometries. | ||
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| Expected keys in the "jx-args.json" file: | ||
| PLOT_GEOMETRY_FILE - the path to the shapefile to convert to GeoJSON | ||
| PLOT_SHAPEFILE - the path to save the GeoJSON to | ||
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| Sample command: | ||
| scif run shp2geojson | ||
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| See also: | ||
| https://github.com/AgPipeline/drone-makeflow/blob/master/README.md | ||
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| %appinstall merge_csv | ||
| # Install dependencies | ||
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| %apprun merge_csv | ||
| /cctools/bin/makeflow \ | ||
| --jx \ | ||
| --jx-args="/scif/apps/src/jx-args.json" \ | ||
| --log-verbose \ | ||
| --retry-count=1 \ | ||
| --change-directory="${SCIF_APPDATA}" \ | ||
| --makeflow-log="${SCIF_APPDATA}/workflow.jx.makeflowlog" \ | ||
| --batch-log="${SCIF_APPDATA}/workflow.jx.batchlog" \ | ||
| ${1} \ | ||
| "/scif/apps/src/merge_csv_workflow.jx" | ||
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| %apphelp merge_csv | ||
| This app searches folders for CSV files and merges them by file name into the output folder | ||
|
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| Expected keys in the "jx-args.json" file: | ||
| MERGECSV_SOURCE - the folder path to look for CSV file | ||
| MERGECSV_TARGET - the folder path to save the merged CSV files to | ||
| MERGECSV_OPTIONS - options for processing CSV files; set to "--help" to display all available options without processing files | ||
|
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| Sample command: | ||
| scif run merge_csv | ||
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| See also: | ||
| https://github.com/AgPipeline/drone-makeflow/blob/master/README.md | ||
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| %appinstall find_files2json | ||
| # Install dependencies | ||
|
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| %apprun find_files2json | ||
| /cctools/bin/makeflow \ | ||
| --jx \ | ||
| --jx-args="/scif/apps/src/jx-args.json" \ | ||
| --log-verbose \ | ||
| --retry-count=1 \ | ||
| --change-directory="${SCIF_APPDATA}" \ | ||
| --makeflow-log="${SCIF_APPDATA}/workflow.jx.makeflowlog" \ | ||
| --batch-log="${SCIF_APPDATA}/workflow.jx.batchlog" \ | ||
| ${1} \ | ||
| "/scif/apps/src/find_files2json_workflow.jx" | ||
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| %apphelp find_files2json | ||
| This app searches folders for files and writes out a JSON file intended to be used as input to a workflow. | ||
| The search assumes the wanted files are located in subfolders off the FILES2JSON_SEARCH_FOLDER. | ||
| If no files matching the search name are found then no JSON file is saved. | ||
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| Expected keys in the "jx-args.json" file: | ||
| FILES2JSON_SEARCH_NAME - the name of the files to locate | ||
| FILES2JSON_SEARCH_FOLDER - the path to the folder to search within | ||
| FILES2JSON_JSON_FILE - the path to the JSON file to write found files to | ||
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| Sample command: | ||
| scif run find_files2json |
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