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SOFT7

Installation

Install the core soft7 package, which supports SOFT7 entities and entity instances, with:

pip install soft7

Some functionality depends on optional dependencies, which are grouped into extras:

  • oteapi: SOFT7 data sources (s7.factories.create_datasource()) and the SOFT7 OTEAPI plugin. These rely on OTEAPI Core and OTELib.
  • graph: Utilities for working with SOFT7 entities as knowledge graphs (s7.graph).

To install soft7 with an extra, e.g., oteapi, run:

pip install 'soft7[oteapi]'

If you use oteapi functionality without the extra installed, an ImportError (s7.exceptions.MissingExtra) is raised that says how to install it.

OTEAPI plugin

The soft7 packages comes with an OTEAPI plugin that allows one to convert any core parser data to a SOFT7 Entity instance. The plugin requires the oteapi extra (see Installation).

To use the plugin, call the 'soft7' functionType function strategy.

Test the plugin

At the root of the repository is a Docker Compose file, which, when run, will start an OTEAPI Service that includes the soft7 OTEAPI plugin.

To start the service, run:

docker compose pull
docker compose up -d

To follow along with the installation of the soft7 package and startup of the OTEAPI Service, run:

docker logs -f soft7-oteapi-1

Press Ctrl+C to stop following the logs.

To eventually stop the services, run:

docker compose down

But first, let's test the plugin.

Open a Python shell, an IPython shell, or a Jupyter Notebook, and run:

from s7.factories import create_datasource

# Let us use an OPTIMADE structure from the Materials Project as our "raw" data source.
# The chosen structure is mp-1228448 (Al2O3):
# https://materialsproject.org/materials/mp-1228448/
# For more information about OPTIMADE, see https://www.optimade.org/
# For more information about the Materials Project, see https://materialsproject.org/
dataresource_config = {
    "downloadUrl": (
        "https://optimade.materialsproject.org/v1/structures/mp-1228448?"
        "response_format=json"
    ),
    "mediaType": "application/json",
}

# We need to setup a mapping configuration to tell the plugin how to map the OPTIMADE
# structure to a SOFT7 Entity instance.
# This requires knowledge of the OPTIMADE structure and the SOFT7 Entity.
# In our case the OPTIMADE structure specification is available at
# https://github.com/Materials-Consortia/OPTIMADE/blob/v1.1.0/optimade.rst#structures-entries
# and the SOFT7 Entity of choice is the `OPTIMADEStructure` Entity, which can be found
# at http://onto-ns.com/meta/1.0/OPTIMADEStructure
mapping_config = {
    "mappingType": "triples",
    "prefixes": {
        "optimade": "https://optimade.materialsproject.org/v1/structures/mp-1228448#",
        "soft7": "http://onto-ns.com/meta/1.0/OPTIMADEStructure#",
    },
    "triples": {
        ("optimade:data.id", "", "soft7:properties.id"),
        ("optimade:data.type", "", "soft7:properties.type"),
        ("optimade:data.attributes", "", "soft7:properties."),
    },
}