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utilities for working with the NIF ontology

Project description

nifstd-tools

PyPI version

Tools for working with the NIF-Ontology.

Installation

The use of nifstd-tools is highly intertwined with the pyontutils respository. If you have a use case (e.g. ontree) where nifstd-tools works as a stand-alone package install it using pip install --user nifstd-tools. Otherwise see below for the full development installation instructions.

Configuration

See pyontutils configuration.

Development Installation

Follow the parent instructions and refer to the rest of this section if you encounter issues.

Note that the optional development packages are not strictly required and if you have installation issues development can proceed normally without them, some database queries will just be slower because they use a pure python mysql connector.

If you are installing a development setup note that mysql-connector (aka mysql-connector-python) often cannot find the files it needs to build. When installing pass them in as environment variables (you may need to adjust exact paths for your system). MYSQLXPB_PROTOBUF_INCLUDE_DIR=/usr/include/google/protobuf MYSQLXPB_PROTOBUF_LIB_DIR=/usr/lib64 MYSQLXPB_PROTOC=/usr/bin/protoc pipenv install --skip-lock. There are some systems on which even this is not sufficient. If you encounter this situation add mysql-connector = "==2.1.6" to [dev-packages] in the Pipfile. And then run the command without environment variables.

If you don't want to use pipenv (which is probably most people) then the quickest way to get up and running with a development install is pip install --user --editable . from the folder that contains this readme.

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