Skip to contents

UlyssesStudy R6 Class

Source: R/Ulysses.R
UlyssesStudy.Rd

Configuration and initialization class for Ulysses study repositories. This class manages the creation and setup of a new study repository, including directory structure, configuration files, and version control initialization.

Details

UlyssesStudy encapsulates the configuration needed to set up a new Ulysses-based study environment. It manages study metadata and database connection blocks. Database schema and credential details are held per-block in DbConfigBlock.

Active Fields

  • repoName: Study repository name (read/write)

  • repoFolder: Parent directory for the repository (read/write)

  • studyMeta: StudyMeta object containing metadata (read/write)

  • dbConnectionBlocks: List of DbConfigBlock objects (read/write)

  • gitRemote: Optional git remote URL (read/write)

  • renvLockFile: Optional path to renv lock file (read/write)

Methods

  • initialize(): Create and configure a new UlyssesStudy instance

  • initUlyssesRepo(): Initialize the full repository structure

Active bindings

repoName

Study repository name. Can be read or set with validation.

repoFolder

Parent directory for the repository. Can be read or set with validation.

dbConnectionBlocks

List of DbConfigBlock objects managing multiple database connections. Can be read or set with class validation.

studyMeta

StudyMeta object containing study metadata and configuration. Can be read or set with class validation.

gitRemote

Optional URL for git remote repository. Can be read or set with validation.

renvLockFile

Optional path to renv lock file for reproducibility. Can be read or set with validation.

Methods

Public methods

Method new()

Initialize a new UlyssesStudy instance with configuration parameters.

Usage

UlyssesStudy$new(
  repoName,
  repoFolder,
  studyMeta,
  dbConnectionBlocks = NULL,
  gitRemote = NULL,
  renvLockFile = NULL
)

Arguments

repoName

Character string. Name of the study repository.

repoFolder

Character string. Parent directory where the repository will be created.

studyMeta

StudyMeta object. Contains study metadata and configuration.

dbConnectionBlocks

List of DbConfigBlock objects. Optional database configurations.

gitRemote

Character string. Optional URL for git remote repository.

renvLockFile

Character string. Optional path to renv lock file for reproducibility.

Returns

Invisibly returns self for method chaining.

Method initUlyssesRepo()

Initialize the complete Ulysses repository structure and configuration.

This method performs the following initialization steps:

  1. Creates the R project directory and Rproj file

  2. Establishes the standard directory structure

  3. Creates initialization files (README, NEWS, configuration files)

  4. Sets up Quarto documentation

  5. Creates main execution file

  6. Initializes agent skills configuration

  7. Initializes git repository

Usage

UlyssesStudy$initUlyssesRepo(verbose = TRUE, openProject = FALSE)

Arguments

verbose

Logical. If TRUE (default), displays informative messages during initialization.

openProject

Logical. If TRUE, opens the project in a new RStudio session after initialization.

Returns

Invisibly returns the path to the initialized repository.

Method clone()

The objects of this class are cloneable with this method.

Usage

UlyssesStudy$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.