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MicaDOI

Export mica datasets and generate DOI for them on DataCite.

Required environment variables

The following code snippets suppose that you have set the following environment variables:

export MICA_USER=administrator
export MICA_PASSWORD=password
export MICA_HOST="https://mica-demo.obiba.org/"

export DATACITE_CLIENT=<my-datacite-client>
export DATACITE_PASSWORD=<my-datacite-password>
export DATACITE_HOST="https://api.test.datacite.org"

In this case, we're using the mica demo server and our DataCite test account. Refer to your department for the datacite credentials.

Usage

Note: when refering to datasets, it is implied that we're talking about the metadata, not the data itself. This tool does not support the download of data for now.

Download a dataset's metadata from a mica instance

With the extract command, we download the cag-baseline dataset and pipe the resulting json into a output/cag-baseline.mica.json file. This file will contain information that will be used to build a DataCite metadata record.

# extract a specific dataset from mica
poetry run python micadoi/ extract \
  --mica-host $MICA_HOST \
  --mica-user $MICA_USER \
  --mica-password $MICA_PASSWORD \
  cag-baseline > output/cag-baseline.mica.json

You can inspect the resulting json. The tool extracts the dataset metadata, its related study and variables.

Update config.json with the missing information

Some metadata is not present in mica. To fix this, a config.json file contains all the required metadata and must be updated by the user to generate a correct DOI.

See the example config.json file. All fields are required for now. The will become optional if the metadata is somehow added to mica.

Generate the DOI

It's not time to generate our DOI from our downloaded metadata. We specify the credentials and the path to out *.mica.json file.

# create a new DOI based on an extracted mica dataset
poetry run python micadoi/ generate-mica-doi \
  --datacite-host $DATACITE_HOST \
  --datacite-user $DATACITE_CLIENT \
  --datacite-password $DATACITE_PASSWORD \
  output/cag-baseline.mica.json > output/cag-baseline.doi.json

The result is piped into a file output/cag-baseline.doi.json. The id found in this json file is the doi.

The DOI is created in draft mode. This means you can access DataCite Fabrica or it's test sibling to inspect, update and publish your DOI.