Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/australianbiocommons/gen3-metadata-templates

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

https://github.com/australianbiocommons/gen3-metadata-templates

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

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

Basic Info
  • Host: GitHub
  • Owner: AustralianBioCommons
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 355 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created about 1 year ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

gen3-metadata-templates

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

installation

bash pip install gen3_metadata_templates

Usage

First lets create a ResolveSchema object, which contains methods and attributes for working with a resolved gen3 schema. ```python from gen3metadatatemplates.templates import * from gen3validator.resolveschema import ResolveSchema

resolver = ResolveSchema("path/to/gen3schema.json") resolver.resolveschema() We then parse the ResolveSchema object to generate an Excel template. python generatexlsxtemplate(resolver=resolver, targetnode="unalignedreadsfile", outputfilename="unalignedreadsfile.xlsx")

some columns are excluded by default, but you can return all by using

generatexlsxtemplate(resolver=resolver, targetnode="unalignedreadsfile", outputfilename="unalignedreadsfile.xlsx", excludecolumns= []) 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. python df = makenodetemplatepd(resolver, node="unalignedreadsfile")

Alternatively you can not exclude any columns

df = makenodetemplatepd( resolver, node="unalignedreadsfile", excludecolumns=[], excluded_nodes=[] ) print(df)

```

Dev Installation

  • Make sure you have Poetry version 2.1.3 installed. bash 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

Owner

  • Name: AustralianBioCommons
  • Login: AustralianBioCommons
  • Kind: organization
  • Email: systems@biocommons.org.au

Documentation for the development, deployment and/or optimisation of key community-endorsed bioinformatics tools and workflows

GitHub Events

Total
  • Release event: 1
  • Push event: 13
  • Create event: 3
Last Year
  • Release event: 1
  • Push event: 13
  • Create event: 3

Dependencies

.github/workflows/build.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • actions/upload-artifact v4 composite
pyproject.toml pypi
requirements.txt pypi