Package index • datom

Connection & Setup

Create connections, initialize repositories

datom_init_repo(): Initialize a datom Repository
datom_clone(): Clone a datom Repository
datom_get_conn(): Get a datom Connection
print(<datom_conn>): Print a datom Connection

Store Objects

Create and inspect storage configuration objects

datom_store(): Create a datom Store
datom_store_s3(): Create an S3 Store Component
datom_store_s3_creds(): Create a Credentials-Only S3 Store Component
datom_store_local(): Create a Local Filesystem Store Component
is_datom_store(): Check if Object is a datom Store
is_datom_store_s3(): Check if Object is an S3 Store Component
is_datom_store_s3_creds(): Check if Object is a Credentials-Only S3 Store Component
is_datom_store_local(): Check if Object is a Local Store Component
print(<datom_store>): Print a datom Store
print(<datom_store_s3>): Print an S3 Store Component
print(<datom_store_s3_creds>): Print a Credentials-Only S3 Store Component
print(<datom_store_local>): Print a Local Store Component

Read & Write

Read and write versioned tables

datom_read(): Read a datom Table
datom_write(): Write a datom Table
datom_check_hashable(): Check Whether a Table Can Be Hashed by datom

Query & Status

List tables, view history, check status

datom_list(): List Available Tables
datom_summary(): Summarize a datom Project
print(<datom_summary>): Print a datom_summary
datom_projects(): List Projects Registered in the Governance Repo
datom_history(): Show Version History
datom_status(): Show Repository Status
datom_get_parents(): Get Parent Lineage for a Table
datom_get_lineage(): Get Lineage for a Table
datom_parent(): Declare a parent for lineage
datom_lineage_union(): Union and deduplicate source_lineage lists

Sync Operations

Batch sync from files, scan manifests, sync metadata to S3

datom_pull(): Pull Latest Changes from Remote
datom_sync(): Sync Files to datom Repository
datom_sync_manifest(): Scan and Prepare Manifest for Sync

Validation

Validate repository structure and git-S3 consistency

datom_validate(): Validate Git-Storage Consistency
is_valid_datom_repo(): Check if Path is a Valid datom Repository

Storage Extension API

Low-level storage and data-repo primitives for package developers (e.g. datomanager). End users should use datom_read / datom_write / datom_repo_delete instead.

datom_storage_list(): List All Objects in a datom Storage Namespace
datom_storage_delete_prefix(): Delete All Objects Under a datom Storage Prefix
datom_storage_copy(): Copy All Objects Between Two datom Storage Namespaces
datom_storage_verify(): Verify a Copy Between Two datom Storage Namespaces
datom_repo_set_data_store(): Rewrite the Data Store Pointer in project.yaml
datom_repo_attach_governance(): Write the Data-Side Governance Attachment Record

Teardown

Permanently remove a project’s data repo and local clone

datom_repo_delete(): Delete the Data GitHub Repository and Local Clone

Example Data

Bundled clinical trial data for examples and vignettes

datom_example_data(): Load Example EDC Data
datom_example_cutoffs(): Monthly Cutoff Dates for Example Study