https://github.com/australianbiocommons/gen3-metadata
User friendly tools for downloading and manipulating gen3 metadata
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 (9.7%) to scientific vocabulary
Repository
User friendly tools for downloading and manipulating gen3 metadata
Basic Info
- Host: GitHub
- Owner: AustralianBioCommons
- License: apache-2.0
- Language: Python
- Default Branch: main
- Size: 306 KB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
gen3-metadata
User friendly tools for downloading and manipulating gen3 metadata
Python Installation
bash
git clone https://github.com/AustralianBioCommons/gen3-metadata.git
bash build.sh
Usage Example
- Notebook can be found in the
example_notebook.ipynbfile - Make sure to select .venv as the kernel in the notebook
```python from gen3metadata.gen3metadata_parser import Gen3MetadataParser
Initialise
keyfile = "path/to/credentials.json" gen3metadata = Gen3MetadataParser(keyfile)
Authenticate
gen3metadata.authenticate()
Fetching data and returning as dataframe
programname = "program1" projectcode = "project1" nodelabel="medicalhistory" pddata = gen3metadata.fetchdatapd(programname, projectcode, nodelabel=nodelabel) pddata
Fetching data and returning as json
jsondata = gen3metadata.fetchdatajson(programname, projectcode, nodelabel=nodelabel) jsondata ```
Running Tests
The tests are written using the pytest framework.
bash
pytest -vv tests/
Installation of the R version of gen3-metadata
You can install the gen3metadata R tool from GitHub with:
r
if (!require("devtools")) install.packages("devtools")
devtools::install_github("AustralianBioCommons/gen3-metadata", subdir = "gen3metadata-R")
The package depends on several other packages, which should hopefully be installed automatically.
If case this doesn't happen, run:
r
install.packages(c("httr", "jsonlite", "jose", "glue"))
Then all you need to do is load the package.
r
library("gen3metadata")
Usage Example
This is a basic example to authenticate and load some data.
``` r
Load the library
library("gen3metadata")
Set the path to the credentials file
keyfilepath <- "path/to/credentials.json"
Create the Gen3 Metadata Parser object
gen3 <- Gen3MetadataParser(keyfilepath)
Authenticate the object
gen3 <- authenticate(gen3)
Load some data
dat <- fetchdata(gen3, programname = "program1", projectcode = "AusDiab", nodelabel = "subject") ```
Owner
- Name: AustralianBioCommons
- Login: AustralianBioCommons
- Kind: organization
- Email: systems@biocommons.org.au
- Website: https://www.biocommons.org.au/
- Repositories: 17
- Profile: https://github.com/AustralianBioCommons
Documentation for the development, deployment and/or optimisation of key community-endorsed bioinformatics tools and workflows
GitHub Events
Total
- Create event: 7
- Release event: 1
- Issues event: 2
- Watch event: 1
- Delete event: 2
- Issue comment event: 2
- Member event: 1
- Push event: 25
- Pull request review comment event: 1
- Pull request review event: 2
- Pull request event: 5
- Fork event: 1
Last Year
- Create event: 7
- Release event: 1
- Issues event: 2
- Watch event: 1
- Delete event: 2
- Issue comment event: 2
- Member event: 1
- Push event: 25
- Pull request review comment event: 1
- Pull request review event: 2
- Pull request event: 5
- Fork event: 1
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 1
pypi.org: gen3-metadata
User friendly tools for downloading and manipulating gen3 metadata
- Documentation: https://gen3-metadata.readthedocs.io/
- License: Apache 2.0
-
Latest release: 1.1.0
published 12 months ago