Migrate Commands - Pidgeon Health

Migrate moves healthcare data between systems via FHIR R4 Bulk Data Access (NDJSON per the HL7 IG). v1 ships the run export workflow reading from Centricity / athenaPractice 23.0 FHIR_* views.

Migrate requires a Pidgeon account sign-in. It is built for migration projects, not synthetic test data — for populations, see Flock.

pidgeon migrate run

Export from a source EHR to FHIR R4 Bulk Data NDJSON — one file per resource type plus a manifest.json conforming to the HL7 FHIR Bulk Data Access IG.

pidgeon migrate run --source <connection-string> --output <dir> [options]

Flag	Type	Default	Description
`--source`	string	Required	Source DB connection string (Postgres or SQL Server; auto-detected by shape)
`--output`	string	Required	Output directory. Created if missing; existing files overwritten unless `--resume`
`--mapping`	string	sane defaults	Mapping YAML for per-field retain/redact/date-shift policy (per-customer override)
`--source-adapter`	string	`centricity`	Source EHR adapter key
`--resources`	string	Patient,Encounter,Observation,Condition,MedicationRequest,Procedure	Comma-separated resource list
`--since`	string	—	Incremental cursor (ISO 8601). v1: recorded in the manifest, full export still runs
`--batch-size`	int	`1000`	NDJSON flush batch size
`--deidentify`	flag	off	Run emitted resources through de-identification before write; cross-resource references stay coherent
`--deident-salt`	string	random	Deterministic hashing salt for cross-run reference consistency
`--deident-date-shift`	string	—	Uniform date shift, `+Nd` or `-Nd` (e.g. `+30d`)
`--resume`	flag	off	Resume from `.checkpoint.json` in the output directory
`--dry-run`	flag	off	Read + transform + reconcile without writing NDJSON; manifest still emitted

# Full export with de-identification
pidgeon migrate run --source "Host=localhost;Database=centricity;..." --output ./export --deidentify --deident-date-shift +30d

# Validate the mapping before a real run
pidgeon migrate run --source "Host=localhost;Database=centricity;..." --output ./export --dry-run

# Resume an interrupted export
pidgeon migrate run --source "Host=localhost;Database=centricity;..." --output ./export --resume

pidgeon migrate analyst

Deterministic migration analysis: assess a source, review the mapping and loss catalog, convert a bounded sample, cluster exceptions, analyze reconciliation, and assemble cutover-readiness evidence. Read/derive-only — results are local evidence artifacts.

pidgeon migrate analyst <subcommand> [options]

Subcommands cover source assessment, mapping-plan review, bounded sample conversion, exception clustering, reconciliation analysis, and cutover-readiness evidence. Sample sizes are bounded (1–25 rows) so a run is fast and reproducible.

pidgeon migrate to-xds

Read a FHIR R4 bundle, generate a C-CDA, and submit it to an IHE XDS.b registry via ITI-41 Provide and Register. With --verify (default), it confirms the round-trip by ITI-18 FindDocuments + ITI-43 Retrieve and asserts the document is byte-identical.

pidgeon migrate to-xds --bundle <bundle.json> [options]

Flag	Type	Default	Description
`--bundle`	string	Required	Path to a FHIR R4 bundle JSON file
`--registry`	string	mock-network default	XDS toolkit base URL
`--verify`	flag	on	Assert a byte-identical ITI-18/ITI-43 round-trip after submit

Desktop app

The Migrate desktop app runs the same run workflow with a preflight checklist, a live migration log, and reconciliation — see Get started with Migrate.

​pidgeon migrate run

​pidgeon migrate analyst

​pidgeon migrate to-xds

​Desktop app

pidgeon migrate run

pidgeon migrate analyst

pidgeon migrate to-xds

Desktop app