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rDataPipeline (version 0.60.0)

Functions to Interact with the 'FAIR Data Pipeline'

Description

R implementation of the 'FAIR Data Pipeline API'. The 'FAIR Data Pipeline' is intended to enable tracking of provenance of FAIR (findable, accessible and interoperable) data used in epidemiological modelling.

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Version

Install

install.packages('rDataPipeline')

Monthly Downloads

197

Version

0.60.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/FAIRDataPipeline/rDataPipeline

Homepage

https://www.fairdatapipeline.org/rDataPipeline/

Maintainer

Ryan Field

Last Published

October 8th, 2024

Functions in rDataPipeline (0.60.0)

fdp_resolve_read

fdp_resolve_read

fdp_resolve_write

fdp_resolve_write

find_write_match

Find matching write aliases in config file

Get H5 file components

Finalise code run

create_version_number

Create version number

find_read_match

Find matching read aliases in config file

Get entity from url

Get fields from table

Initialise code run

Calculate hash from file

check_local_repo

check_local_repo

get_dataproduct

get_dataproduct

Post entry to file_type table

Get tables from registry

get_table_queryable

Get queryable fields

increment_filename

increment_filename

get_table_readable

Get readable fields

get_storage_location

Get storage location from url

Return all fields associated with a table entry in the data registry

get_table_optional

Get optional fields

Post entry to keyword table

List files in GitHub repository

get_github_hash

Get current GitHub hash

new_storage_location

Post entry to storage_location table

get_max_version

get_max_version

Post entry to licence table

Post entry to issue table

Link path to external format data

Post entry to object table

remove_empty_parents

remove_empty_parents

Post entry to namespace table

Check whether fields are queryable

Read array component from HDF5 file

raise_issue_repo

Raise issue with remote repository

raise_issue_config

Raise issue with config file

new_storage_root

Post entry to storage_root table

write_distribution

Write distribution component to TOML file

raise_issue_script

Raise issue with submission script

Return all entries posted to a table in the data registry

read_distribution

Read distribution component from TOML file

Write estimate component to TOML file

Link path for external format data

get_table_required

Get required fields

Write table component to HDF5 file

validate_fields

Validate fields

rDataPipeline-package

get_table_writable

Get writable fields

register_issue_dataproduct

register_issue_dataproduct

Post entry to author table

new_user_author

Post entry to user_author table

register_issue_script

register_issue_script

new_object_component

Post entry to object_component table

Check whether paper exists

Post entry to code_run table

new_quality_controlled

Post entry to quality_controlled table

new_data_product

Post entry to data_product table

Write array component to HDF5 file

new_external_object

Post entry to external_object table

Patch entry in data registry

new_code_repo_release

Post entry to code_repo_release table

Read table component from HDF5 file

Post entry to data registry

Read estimate component from TOML file

resolve_version

resolve_version

resolve_data_product

check_dataproduct_exists

check_dataproduct_exists

Check if entry exists in the data registry

check_table_exists

Check if table exists

check_yaml_write

check_yaml_write

download_from_database

Download source file from database

download_from_url

Download source file from URL