im-data-manager-metadata 0.0.6

A framework for Informatics Matters dataset metadata

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 'label' -lv='blob' -af=test/output

• 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 -fo='squonk2-job' -fp='minimizedAffinity,number,Binding affinity
                        predicted by smina using the vinardo scoring function,true,true'
                        -fd='Run smina docking' -af=test/output

• Creates a service execution annotation in an annotations.json file placed in test/output.

>>> python md_manage.py se -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' -af=test/output