gen3_metadata_templates 1.0.1

Create Gen3 Metadata Submission Templates from a Gen3 JSON Schema

gen3-metadata-templates

Tool to create metadata submission templates from a gen3 json schema.

installation

pip install gen3_metadata_templates

Usage

First lets create a ResolveSchema object, which contains methods and attributes for working with a resolved gen3 schema.

from gen3_metadata_templates.templates import *
from gen3_validator.resolve_schema import ResolveSchema

resolver = ResolveSchema("path/to/gen3_schema.json")
resolver.resolve_schema()

We then parse the ResolveSchema object to generate an Excel template.

generate_xlsx_template(resolver=resolver, target_node="unaligned_reads_file", output_filename="unaligned_reads_file.xlsx")

# some columns are excluded by default, but you can return all by using
generate_xlsx_template(resolver=resolver, target_node="unaligned_reads_file", output_filename="unaligned_reads_file.xlsx", exclude_columns= [])

You can also generate a template for a specific node. By default, some columns are excluded. Note: If the node is "program" or "project", it will be excluded and the function will return None. The function returns a pandas DataFrame.

df = make_node_template_pd(resolver, node="unaligned_reads_file")

# Alternatively you can not exclude any columns
df = make_node_template_pd(
    resolver,
    node="unaligned_reads_file",
    exclude_columns=[],
    excluded_nodes=[]
)
print(df)

Dev Installation

• Make sure you have Poetry version 2.1.3 installed.

git clone https://github.com/AustralianBioCommons/gen3-metadata-templates.git
cd gen3-metadata-templates
pip install poetry
poetry install
eval $(poetry env activate)
poetry run pytest -vv