Add script to build access requirement JSON schemas and support registering + binding in Synapse

[Bankso]

• generate_duo_schema.py uses a pre-defined CSV specification to build JSON schemas that allow access requirements to be conditionally activated. CSV spec is described here.

Help text for current script version (click details):

usage: generate_duo_schema.py [-h] [-t TITLE] [-v VERSION] [-o ORG_ID] [-a ACCESS_REQUIREMENT] [-g GRANT_ID] [-m]
                              [-gc GRANT_COL] [-s STUDY_ID] [-sc STUDY_COL] [-d DATA_TYPE] [-dc DATA_COL]
                              [-p SPECIES_TYPE] [-pc SPECIES_COL]
                              csv_path output_path

  Generate Access Requirement JSON Schema from Data Dictionary CSV

  positional arguments:
    csv_path              Path to the data_dictionary.csv. See and example at https://github.com/Sage-Bionetworks/governanceDUO/blob/main/access_requirement_JSON/README.md
    output_path           Path to output directory for the JSON schema

  options:
  -h, --help            show this help message and exit
  -t TITLE, --title TITLE
                        Schema title
  -v VERSION, --version VERSION
                        Schema version
  -o ORG_ID, --org_id ORG_ID
                        Organization ID for $id field
  -a ACCESS_REQUIREMENT, --access_requirement ACCESS_REQUIREMENT
                        Access requirement ID to select conditions for from reference table. If nothing is provided, the
                        JSON schema will include all applicable conditions listed in the input table.
  -g GRANT_ID, --grant_id GRANT_ID
                        Grant number to select conditions for from reference table. If nothing is provided, the JSON
                        schema will include all conditions listed in the input table.
  -m, --multi_condition
                        Boolean. Generate schema with multiple conditions defined in the CSV
  -gc GRANT_COL, --grant_col GRANT_COL
                        Name of the column in the DCC AR data dictionary that will contain the identifier for the grant
  -s STUDY_ID, --study_id STUDY_ID
                        Study ID to select conditions for from reference table. If nothing is provided, the JSON schema
                        will include all applicable studies listed in the input table.
  -sc STUDY_COL, --study_col STUDY_COL
                        Name of the column in the DCC AR data dictionary that will contain the identifier for the study
  -d DATA_TYPE, --data_type DATA_TYPE
                        Data type to select conditions for from reference table. If nothing is provided, the JSON schema
                        will include all applicable data types listed in the input table.
  -dc DATA_COL, --data_col DATA_COL
                        Name of the column in the DCC AR data dictionary that will contain the identifier for the data
                        type
  -p SPECIES_TYPE, --species_type SPECIES_TYPE
                        Species to select conditions for from reference table. If nothing is provided, the JSON schema
                        will include all applicable species listed in the input table.
  -pc SPECIES_COL, --species_col SPECIES_COL
                        Name of the column in the DCC AR data dictionary that will contain the identifier for the
                        species

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• Updated synapse_json_schema_bind.py to generalize input format and support registering and/or binding non-AR JSON schemas. Note the JSON schema file naming conventions defined on line 136 and 137 (can be updated later, if needed):

Non-AR schema example: mc2.DatasetView-v1.0.0-schema.json
AR schema example: MC2.AccessRequirement-CA000001-v3.0.2-schema.json)

Help text for current script version (click details):

usage: synapse_json_schema_bind.py [-h] [-t T] [-l L] [-p P] [-n N] [-ar] [--no_bind]

options:
  -h, --help  show this help message and exit
  -t T        Synapse Id of an entity to which a schema will be bound.
  -l L        The URL for the JSON schema to be bound to the requested entity.
  -p P        The file path for the JSON schema to be bound to the requested entity.
  -n N        The name of the organization with which the JSON schema should be associated. Default: 'Example
              Organization'.
  -ar         Indicates if the schema includes Access Requirement information.
  --no_bind   Indicates the schema should not be bound to the entity.