> ## Documentation Index
> Fetch the complete documentation index at: https://docs.pidgeon.health/llms.txt
> Use this file to discover all available pages before exploring further.

# Migrate Commands

> Export healthcare data to FHIR R4 Bulk Data NDJSON, with de-identification, reconciliation, and resume.

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.

<Note>Migrate requires a Pidgeon account sign-in. It is built for migration projects, not synthetic test data — for populations, see [Flock](/cli/flock-commands).</Note>

## 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.

```bash theme={null}
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                           |

```bash theme={null}
# 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.

```bash theme={null}
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.

```bash theme={null}
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](/getting-started/migrate).