A framework for Informatics Matters dataset metadata
Project description
A metadata framework package for the Data Tier Data Manager service. The im-data-manager-metadata package is a set of utilities employed by the Informatics Matters Data-Manager service as a metadata framework for molecular datasets.
Dependencies
PyYAML>=5.3
jsonpickle>=2.0.0
Running the Unit Tests
>>> python -m venv ~/.venv/data-manager-metadata >>> source ~/.venv/data-manager-metadata/bin/activate >>> pip install --upgrade pip >>> pip install -r package-requirements.txt >>> python -m unittest test.test
Running the Command Line Interface md-manage.py
The data manager metadata command line interface can be used by applications to add annotations to the Metadata by means of an annotations.json files that can be uploaded.
help functions. Note that the annotation_type (lb, fd or se) is required.
>>> python md_manage.py -h >>> python md_manage.py lb -h >>> python md_manage.py fd -h >>> python md_manage.py se -h
Creates a label annotation in an annotations.json file placed in test/output. Note that the label is required. Running the command again will create a second annotation in the same file (i.e. a list of two).
>>> python md_manage.py lb test/output/results.sdf 'foo' -lv='bar'
Creates a FieldsDescriptorAnnotation in an annotations.json file placed in test/output. If the annotations.json file exists it will add it to the list of annotations in the file.
>>> python md_manage.py fd test/output/results.sdf -fo='squonk2-job' -fp='minimizedAffinity,number,Binding affinity predicted by smina using the vinardo scoring function,true,true' -fd='Run smina docking'
Creates a service execution annotation in an annotations.json file placed in test/output.
>>> python md_manage.py se test/output/results.sdf -su=bob -sys='run-smina' -sy='test/input/virtual-screening.yaml' -sp param1=val1 param2=val2 -fo='squonk2-job' -fp='minimizedAffinity,number,Binding affinity predicted,true,true' -fd='Run smina docking'
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