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Metacatalog aggregator

This tool is designed to be used together with the V-FOR-WaTer Metacatalog data loader. It uses a number of data source files along with either a metacatalog entry or JSON dumps of the metadata. The data is aggregated to a target precision (temporal) and spatial resolution and then ingested into a geocube that is stored as a netCDF file.

This tool is based on the Python template for a generic containerized Python tool following the Tool Specification for reusable research software using Docker.

Structure

/
|- in/
|  |- input.json
|- out/
|  |- ...
|- src/
|  |- tool.yml
|  |- run.py
|  |- CITATON.cff
  • input.json are parameters. Whichever framework runs the container, this is how parameters are passed.
  • tool.yml is the tool specification. It contains metadata about the scope of the tool, the number of endpoints (functions) and their parameters
  • run.py is the tool itself
  • CITATION.cff is a citation file that describes the tool and its authors. It is used by the

How to build the image?

You can build the image from within the root of this repo by

docker build -t metacatalog_geocube .

How to run?

This template installs the json2args python package to parse the parameters in the /in/input.json. This assumes that the files are not renamed and not moved and there is actually only one tool in the container. For any other case, the environment variables PARAM_FILE can be used to specify a new location for the parameters.json and TOOL_RUN can be used to specify the tool to be executed. The run.py has to take care of that.

To invoke the docker container directly run something similar to:

docker run --rm -it -v /path/to/local/in:/in -v /path/to/local/out:/out -e TOOL_RUN=geocube metacatalog_geocube

Then, the output will be in your local out and based on your local input folder. Stdout and Stderr are also connected to the host.