add de-identification section to SOF

SUMMARY.md

@@ -327,6 +327,7 @@
   * [Defining flat views with view definitions](modules/sql-on-fhir/defining-flat-views-with-view-definitions.md)
   * [Migrate to the spec-compliant ViewDefinition format](modules/sql-on-fhir/migrate-to-the-spec-compliant-viewdefinition-format.md)
   * [Query data from flat views](modules/sql-on-fhir/query-data-from-flat-views.md)
+  * [De-identification](modules/sql-on-fhir/de-identification.md)
   * [Reference](modules/sql-on-fhir/reference.md)
 * [Integration Toolkit](modules/integration-toolkit/README.md)
   * [C-CDA / FHIR Converter](modules/integration-toolkit/ccda-converter/README.md)

docs/modules/sql-on-fhir/README.md

@@ -4,8 +4,8 @@ description: Create flat SQL views from FHIR resources using ViewDefinitions for
 
 # SQL on FHIR
 
-{% hint style="info" %}
-**SQL on FHIR** engine is currently in **preview**
+{% hint style="warning" %}
+Starting from version **2604**, SQL on FHIR requires **fhir-schema mode** (`fhir.validation.fhir-schema-validation=true`). ViewDefinitions are stored in the FHIR Artifact Registry (FAR), which is only available in fhir-schema mode. Without it, ViewDefinition CRUD, `$run`, `$sql`, and `$materialize` operations will not work.
 {% endhint %}
 
 Performing analysis on FHIR data requires extracting data from deeply nested structures of resources, which may be cumbersome in some cases. To address this problem, Aidbox implements [SQL on FHIR](https://build.fhir.org/ig/FHIR/sql-on-fhir-v2/index.html) specification allowing users to create flat views of their resources in a simple, straightforward way
@@ -22,6 +22,12 @@ Once your flat view is defined and materialized, you can query data from it usin
 
 See [Query data from flat views](./query-data-from-flat-views.md).
 
+## De-identification
+
+Starting from version **2604**, ViewDefinition columns can be annotated with de-identification methods to transform sensitive data during SQL generation. Supported methods include redact, cryptoHash, dateshift, encrypt, substitute, perturb, and custom PostgreSQL functions.
+
+See [De-identification](./de-identification.md).
+
 ## SQL on FHIR reference
 
 To dive deeper into the nuances of using SQL on FHIR in Aidbox, consult the reference page.

docs/modules/sql-on-fhir/de-identification.md

@@ -0,0 +1,334 @@
+# De-identification
+
+Starting from version **2604**, Aidbox supports per-column de-identification in ViewDefinitions via a FHIR extension. When a column has a de-identification extension, the SQL compiler wraps the column expression with a PostgreSQL function that transforms the value before it reaches the output.
+
+This works with all ViewDefinition operations: `$run`, `$sql`, and `$materialize`.
+
+{% hint style="info" %}
+Requires **fhir-schema mode**.
+{% endhint %}
+
+## Extension format
+
+Add the de-identification extension to any column in the `select` array:
+
+```json
+{
+  "name": "birth_date",
+  "path": "birthDate",
+  "extension": [
+    {
+      "url": "http://health-samurai.io/fhir/core/StructureDefinition/de-identification",
+      "extension": [
+        {"url": "method", "valueCode": "dateshift"},
+        {"url": "dateShiftKey", "valueString": "my-secret-key"}
+      ]
+    }
+  ]
+}
+```
+
+The extension uses sub-extensions for the method and its parameters. The `method` sub-extension is required and specifies which de-identification method to apply.
+
+## Methods
+
+### redact
+
+Replaces the value with NULL. No parameters.
+
+```json
+{"url": "method", "valueCode": "redact"}
+```
+
+### cryptoHash
+
+Replaces the value with its HMAC-SHA256 hash (hex-encoded). Deterministic — same input always produces the same hash. One-way, cannot be reversed.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| cryptoHashKey | string | yes | HMAC secret key |
+
+```json
+[
+  {"url": "method", "valueCode": "cryptoHash"},
+  {"url": "cryptoHashKey", "valueString": "my-hash-key"}
+]
+```
+
+### dateshift
+
+Shifts date and dateTime values by a deterministic offset derived from the resource id. All dates within the same resource shift by the same number of days, preserving temporal relationships. The offset range is -50 to +50 days.
+
+Year-only values (`"2000"`) and year-month values (`"2000-06"`) cannot be shifted meaningfully and are replaced with NULL.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| dateShiftKey | string | yes | HMAC key used to compute the per-resource offset |
+
+```json
+[
+  {"url": "method", "valueCode": "dateshift"},
+  {"url": "dateShiftKey", "valueString": "my-shift-key"}
+]
+```
+
+### birthDateSafeHarbor
+
+Intended **only for `Patient.birthDate`**. Behaves like `dateshift` but returns NULL when the birth date implies the patient is over 89 years old, per HIPAA Safe Harbor rule [45 CFR 164.514(b)(2)(i)(C)](https://www.ecfr.gov/current/title-45/subtitle-A/subchapter-C/part-164/subpart-E/section-164.514).
+
+Applying this method to any other date column is semantically incorrect — the function computes `age(current_date, input)` and treats the input as a birth date. Use plain `dateshift` for non-birth-date fields.
+
+Because the function depends on `current_date`, it is marked [`STABLE`](https://www.postgresql.org/docs/current/xfunc-volatility.html) rather than `IMMUTABLE` — PostgreSQL guarantees it returns the same result within a single transaction, but the result may differ between transactions as the current date changes. This means the age cutoff re-evaluates on every query.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| dateShiftKey | string | yes | HMAC key used to compute the per-resource offset |
+
+```json
+[
+  {"url": "method", "valueCode": "birthDateSafeHarbor"},
+  {"url": "dateShiftKey", "valueString": "my-shift-key"}
+]
+```
+
+### encrypt
+
+AES-128-CBC encrypts the value and returns a base64-encoded string. Reversible with the key. Uses a zero initialization vector for deterministic output — same plaintext always produces the same ciphertext.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| encryptKey | string | yes | Hex-encoded AES-128 key (32 hex characters = 16 bytes) |
+
+```json
+[
+  {"url": "method", "valueCode": "encrypt"},
+  {"url": "encryptKey", "valueString": "0123456789abcdef0123456789abcdef"}
+]
+```
+
+{% hint style="warning" %}
+**Key management.** Cryptographic keys (`cryptoHashKey`, `dateShiftKey`, `encryptKey`) are stored as plaintext strings inside the ViewDefinition resource. Anyone with read access to the ViewDefinition can see the keys. Restrict access using [AccessPolicy](../../access-control/authorization/README.md).
+{% endhint %}
+
+{% hint style="warning" %}
+**Encryption limitations.** `encrypt` uses AES-128-CBC with a zero initialization vector. Encryption is deterministic — same plaintext always produces same ciphertext, which is useful for consistent de-identification but leaks frequency information. Not suitable for general-purpose encryption.
+{% endhint %}
+
+### substitute
+
+Replaces the value with a fixed string.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| replaceWith | string | yes | Replacement value |
+
+```json
+[
+  {"url": "method", "valueCode": "substitute"},
+  {"url": "replaceWith", "valueString": "REDACTED"}
+]
+```
+
+### perturb
+
+Adds random noise to numeric values. The result is non-deterministic — each query produces different output.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| span | decimal | no | Noise magnitude. Default: 1.0 |
+| rangeType | code | no | `fixed` (absolute noise) or `proportional` (relative to value). Default: `fixed` |
+| roundTo | integer | no | Decimal places to round to. 0 means integer. Default: 0 |
+
+With `fixed` range type, noise is in the range `±span/2`. With `proportional`, noise is `±(span × value)/2`. Any other `rangeType` value raises a SQL error.
+
+```json
+[
+  {"url": "method", "valueCode": "perturb"},
+  {"url": "span", "valueDecimal": 10},
+  {"url": "rangeType", "valueCode": "fixed"},
+  {"url": "roundTo", "valueInteger": 0}
+]
+```
+
+### custom_function
+
+Applies a user-provided PostgreSQL function. The function must already exist in the database. Its first argument is the column value cast to text. An optional second argument can be passed via `custom_arg`.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| custom_function | string | yes | PostgreSQL function name. Must match `^[a-zA-Z][a-zA-Z0-9_.]*$` |
+| custom_arg | any primitive | no | Optional second argument, passed as a FHIR sub-extension using the appropriate `value[x]` type: `valueString`, `valueInteger`, `valueDecimal`, `valueBoolean`, or `valueCode` |
+
+```json
+[
+  {"url": "method", "valueCode": "custom_function"},
+  {"url": "custom_function", "valueString": "left"},
+  {"url": "custom_arg", "valueInteger": 4}
+]
+```
+
+This example uses the built-in PostgreSQL `left` function to keep only the first 4 characters (e.g. extracting just the year from a date string).
+See also: [Writing custom PostgreSQL functions](#writing-custom-postgresql-functions)
+
+## Example ViewDefinition
+
+A complete ViewDefinition that de-identifies Patient data:
+
+```json
+{
+  "resourceType": "ViewDefinition",
+  "id": "deident-patients",
+  "name": "deident_patients",
+  "status": "active",
+  "resource": "Patient",
+  "select": [{
+    "column": [{
+      "name": "id",
+      "path": "id",
+      "extension": [{
+        "url": "http://health-samurai.io/fhir/core/StructureDefinition/de-identification",
+        "extension": [{
+          "url": "method",
+          "valueCode": "cryptoHash"
+        }, {
+          "url": "cryptoHashKey",
+          "valueString": "patient-hash-key"
+        }]
+      }]
+    }, {
+      "name": "gender",
+      "path": "gender"
+    }, {
+      "name": "birth_date",
+      "path": "birthDate",
+      "extension": [{
+        "url": "http://health-samurai.io/fhir/core/StructureDefinition/de-identification",
+        "extension": [{
+          "url": "method",
+          "valueCode": "dateshift"
+        }, {
+          "url": "dateShiftKey",
+          "valueString": "date-shift-key"
+        }]
+      }]
+    }]
+  }, {
+    "forEachOrNull": "name",
+    "select": [{
+      "column": [{
+        "name": "family",
+        "path": "family",
+        "extension": [{
+          "url": "http://health-samurai.io/fhir/core/StructureDefinition/de-identification",
+          "extension": [{
+            "url": "method",
+            "valueCode": "redact"
+          }]
+        }]
+      }]
+    }]
+  }, {
+    "forEachOrNull": "address",
+    "select": [{
+      "column": [{
+        "name": "postal_code",
+        "path": "postalCode",
+        "extension": [{
+          "url": "http://health-samurai.io/fhir/core/StructureDefinition/de-identification",
+          "extension": [{
+            "url": "method",
+            "valueCode": "substitute"
+          }, {
+            "url": "replaceWith",
+            "valueString": "000"
+          }]
+        }]
+      }]
+    }]
+  }]
+}
+```
+
+In this example:
+
+- `id` is replaced with a consistent hash
+- `gender` passes through unchanged (no extension)
+- `birthDate` is shifted by a deterministic offset per patient
+- `name.family` is redacted (NULL)
+- `address.postalCode` is replaced with "000"
+
+The result from the `$run` operation would look like this:
+
+| `id`                                                             | `gender` | `birth_date` | `family` | `postal_code` |
+|------------------------------------------------------------------|----------|--------------|----------|---------------|
+| a9c063ce560ab35c2156d4bf153457d8c7b0ad6325c1c4112b34eb7147aaa8f9 | female   | 1985-03-02   | null     | 000           |
+| 6e7dfba4a51c359ead0afd9e3ff542c9417505957bf374e510eb37ec020fbc12 | male     | 1952-11-12   | null     | 000           |
+| 27fb6fd29c5657c1a122aa1ae28cdfc5e10b202c6dc7d498cec72609b3a1b447 | female   | 1930-05-08   | null     | 000           |
+
+## Materialization restriction
+
+A ViewDefinition that contains any de-identification extension can only be materialized as a `table`. Attempting to materialize as `view` or `materialized-view` returns HTTP 422 with an OperationOutcome:
+
+This restriction exists because PostgreSQL stores the full view definition (including the compiled SQL with embedded keys) in `pg_views.definition` and `pg_matviews.definition`. Any user with `SELECT` on those catalogs would see the `cryptoHashKey`, `dateShiftKey`, or `encryptKey` values in plaintext. Tables materialize the transformed data only, leaving the keys inside the ViewDefinition resource itself (which is access-controlled).
+
+`$run` and `$sql` are unaffected — they return data or SQL strings directly without storing anything in system catalogs.
+
+## Pre-built ViewDefinitions
+
+The IG package `io.health-samurai.de-identification.r4` provides ready-made Safe Harbor ViewDefinitions for common FHIR R4 resource types. Install it via [Artefact Registry](../../artifact-registry/artifact-registry-overview.md) ("FHIR packages" in Aidbox UI):
+
+| Resource | Use |
+|----------|-----|
+| Patient | Uses `birthDateSafeHarbor` on `birthDate`, cryptoHash on `id`, redact on name/address identifiers |
+| Encounter, Condition, Observation | `dateshift` on clinical dates, cryptoHash on references |
+| Claim, ExplanationOfBenefit | `dateshift` on billable periods |
+| AllergyIntolerance, DiagnosticReport, MedicationRequest, MedicationDispense, MedicationAdministration, Immunization, Procedure, Specimen, DocumentReference | Same general approach |
+| Practitioner, Location | Identifier redaction |
+
+Install the package via FHIR package management and use these ViewDefinitions directly, or copy and customize them. Every cryptographic key parameter in the pre-built VDs is blank (`""`) — you must set real keys before using them for actual de-identification.
+
+## Using the UI
+
+The ViewDefinition builder in Aidbox UI includes a de-identification picker on each column. Click the shield icon next to a column's path to open the configuration popover.
+
+![De-identification picker in the ViewDefinition Builder](../../../assets/deident-viewdefinition-builder.png)
+
+When a de-identification method is configured, the shield icon turns blue. Hovering shows the current method name.
+
+## Writing custom PostgreSQL functions
+
+Custom functions referenced via `custom_function` must:
+
+- Accept `text` as the first argument (the column value)
+- Optionally accept a second argument of any type (passed via `custom_arg`)
+- Already exist in the database before the ViewDefinition is executed
+
+Example:
+
+```sql
+CREATE OR REPLACE FUNCTION my_mask(value text)
+RETURNS text LANGUAGE sql IMMUTABLE PARALLEL SAFE AS $$
+  SELECT CASE
+    WHEN value IS NULL THEN NULL
+    ELSE left(value, 1) || repeat('*', greatest(length(value) - 1, 0))
+  END;
+$$;
+```
+
+Then reference it in a column:
+
+```json
+{
+  "url": "http://health-samurai.io/fhir/core/StructureDefinition/de-identification",
+  "extension": [
+    {"url": "method", "valueCode": "custom_function"},
+    {"url": "custom_function", "valueString": "my_mask"}
+  ]
+}
+```
+
+See also:
+
+- [Defining flat views with view definitions](./defining-flat-views-with-view-definitions.md)
+- [$run operation](./operation-run.md)
+- [$materialize operation](./operation-materialize.md)

docs/modules/sql-on-fhir/operation-materialize.md

@@ -8,7 +8,7 @@ description: Materializing SQL-on-FHIR ViewDefinitions as database tables, views
 {% endhint %}
 
 {% hint style="warning" %}
-When running Aidbox not in FHIRSchema mode, please be aware that input parameters for the `$materialize` operation are not validated against FHIR specifications.
+Requires **fhir-schema mode**.
 {% endhint %}
 
 {% hint style="info" %}

docs/modules/sql-on-fhir/operation-run.md

@@ -4,7 +4,7 @@ description: Using the $run operation to execute SQL-on-FHIR ViewDefinitions
 # $run operation
 
 {% hint style="warning" %}
-When running Aidbox not in FHIRSchema mode, please be aware that input parameters for the `$run` operation are not validated against FHIR specifications.
+Requires **fhir-schema mode**.
 {% endhint %}
 
 {% hint style="info" %}