Engagement/jessica/15405 deidentification enrichment

prime-router/src/main/kotlin/cli/PIIRemovalCommands.kt

@@ -0,0 +1,211 @@
+package gov.cdc.prime.router.cli
+
+import com.github.ajalt.clikt.core.CliktCommand
+import com.github.ajalt.clikt.core.CliktError
+import com.github.ajalt.clikt.parameters.options.option
+import com.github.ajalt.clikt.parameters.options.required
+import com.github.ajalt.clikt.parameters.types.file
+import fhirengine.engine.CustomFhirPathFunctions
+import gov.cdc.prime.router.common.JacksonMapperUtilities
+import gov.cdc.prime.router.fhirengine.translation.hl7.FhirTransformer
+import gov.cdc.prime.router.fhirengine.translation.hl7.utils.FhirPathUtils
+import gov.cdc.prime.router.fhirengine.utils.FhirTranscoder
+import org.hl7.fhir.r4.model.Bundle
+import org.hl7.fhir.r4.model.ContactPoint
+import org.hl7.fhir.r4.model.Organization
+import org.hl7.fhir.r4.model.Organization.OrganizationContactComponent
+import org.hl7.fhir.r4.model.Patient
+import org.hl7.fhir.r4.model.Patient.ContactComponent
+import org.hl7.fhir.r4.model.Practitioner
+import org.hl7.fhir.r4.model.StringType
+
+class PIIRemovalCommands : CliktCommand(
+    name = "piiRemoval",
+    help = "Remove PII"
+) {
+    /**
+     * The input file to process.
+     */
+    private val inputFile by option("-i", "--input-file", help = "Input file to process")
+        .file(true, canBeDir = false, mustBeReadable = true).required()
+
+    /**
+     * Output file to write the data with PII removed.
+     */
+    private val outputFile by option("-o", "--output-file", help = "output file")
+        .file()
+
+    /**
+     * FHIR paths for ids to remove
+     */
+    val idPaths = arrayListOf(
+        "Bundle.entry.resource.ofType(Patient).identifier.value",
+        "Bundle.entry.resource.ofType(ServiceRequest).requester.resolve().practitioner.resolve().identifier.value",
+        "Bundle.entry.resource.ofType(DiagnosticReport).identifier.value"
+    )
+
+    /**
+     * Method called when the command is run
+     */
+    override fun run() {
+        // Read the contents of the file
+        val contents = inputFile.inputStream().readBytes().toString(Charsets.UTF_8)
+        if (contents.isBlank()) throw CliktError("File ${inputFile.absolutePath} is empty.")
+
+        // Check on the extension of the file for supported operations
+        if (inputFile.extension.uppercase() != "FHIR") {
+            throw CliktError("File ${inputFile.absolutePath} is not a FHIR file.")
+        }
+        var bundle = FhirTranscoder.decode(contents)
+
+        bundle.entry.map { it.resource }.filterIsInstance<Patient>()
+            .forEach { patient ->
+                patient.name.forEach { name ->
+                    name.given = mutableListOf(StringType(getFakeValueForElementCall("PERSON_GIVEN_NAME")))
+                }
+                patient.address.forEach { address ->
+                    address.line = mutableListOf(StringType(getFakeValueForElementCall("STREET")))
+                }
+                patient.telecom.forEach { telecom ->
+                    handleTelecom(telecom)
+                }
+                patient.contact.forEach { contact ->
+                    handlePatientContact(contact)
+                }
+            }
+
+        bundle.entry.map { it.resource }.filterIsInstance<Organization>()
+            .forEach { organization ->
+            organization.address.forEach { address ->
+                address.line = mutableListOf(StringType(getFakeValueForElementCall("STREET")))
+            }
+            organization.telecom.forEach { telecom ->
+                handleTelecom(telecom)
+            }
+            organization.contact.forEach { contact ->
+               handleOrganizationalContact(contact)
+            }
+        }
+
+        bundle.entry.map { it.resource }.filterIsInstance<Practitioner>()
+            .forEach { practitioner ->
+                practitioner.address.forEach { address ->
+                    address.line = mutableListOf(StringType(getFakeValueForElementCall("STREET")))
+                    address.city = getFakeValueForElementCallUsingGeoData("CITY", address.state)
+                    address.postalCode = getFakeValueForElementCallUsingGeoData("POSTAL_CODE", address.state)
+                    address.district = getFakeValueForElementCallUsingGeoData("COUNTY", address.state)
+                }
+                practitioner.telecom.forEach { telecom ->
+                    handleTelecom(telecom)
+                }
+                practitioner.name.forEach { name ->
+                    name.given = mutableListOf(StringType(getFakeValueForElementCall("PERSON_GIVEN_NAME")))
+                }
+            }
+
+        bundle = FhirTransformer("classpath:/metadata/fhir_transforms/common/remove-pii-enrichment.yml").process(bundle)
+
+        val jsonObject = JacksonMapperUtilities.defaultMapper
+            .readValue(FhirTranscoder.encode(bundle), Any::class.java)
+        var prettyText = JacksonMapperUtilities.defaultMapper.writeValueAsString(jsonObject)
+        prettyText = replaceIds(bundle, prettyText)
+
+        // Write the output to the screen or a file.
+        if (outputFile != null) {
+            outputFile!!.writeText(prettyText, Charsets.UTF_8)
+        }
+        echo("Wrote output to ${outputFile!!.absolutePath}")
+    }
+
+    /**
+     * Replaces the patient contact PII data
+     */
+    private fun handlePatientContact(contact: ContactComponent): ContactComponent {
+        contact.name.given = mutableListOf(StringType(getFakeValueForElementCall("PERSON_GIVEN_NAME")))
+        contact.name.family = getFakeValueForElementCall("PERSON_FAMILY_NAME")
+        contact.address.line = mutableListOf(StringType(getFakeValueForElementCall("STREET")))
+        contact.address.city = getFakeValueForElementCallUsingGeoData("CITY", contact.address.state)
+        contact.address.postalCode = getFakeValueForElementCallUsingGeoData("POSTAL_CODE", contact.address.state)
+        contact.address.district = getFakeValueForElementCallUsingGeoData("COUNTY", contact.address.state)
+        contact.telecom.forEach { telecom ->
+            handleTelecom(telecom)
+        }
+        return contact
+    }
+
+    /**
+     * Replaces the organizational contact PII. Unfortunately needs to be repeated because they do not share a common
+     * ancestor
+     */
+    private fun handleOrganizationalContact(contact: OrganizationContactComponent): OrganizationContactComponent {
+        contact.name.given = mutableListOf(StringType(getFakeValueForElementCall("PERSON_GIVEN_NAME")))
+        contact.name.family = getFakeValueForElementCall("PERSON_FAMILY_NAME")
+        contact.address.line = mutableListOf(StringType(getFakeValueForElementCall("STREET")))
+        contact.address.city = getFakeValueForElementCallUsingGeoData("CITY", contact.address.state)
+        contact.address.postalCode = getFakeValueForElementCallUsingGeoData("POSTAL_CODE", contact.address.state)
+        contact.address.district = getFakeValueForElementCallUsingGeoData("COUNTY", contact.address.state)
+        contact.telecom.forEach { telecom ->
+            handleTelecom(telecom)
+        }
+        return contact
+    }
+
+    /**
+     * Replaces PII in a telecom
+     */
+    private fun handleTelecom(telecom: ContactPoint): ContactPoint {
+        if (telecom.system == ContactPoint.ContactPointSystem.EMAIL) {
+            telecom.value = getFakeValueForElementCall("EMAIL")
+        } else if (telecom.system == ContactPoint.ContactPointSystem.PHONE ||
+            telecom.system == ContactPoint.ContactPointSystem.FAX
+        ) {
+            telecom.value = getFakeValueForElementCall("TELEPHONE")
+        }
+        return telecom
+    }
+
+    /**
+     * Replaces the required IDs in the bundle
+     */
+    private fun replaceIds(bundle: Bundle, prettyText: String): String {
+        var updatedBundle = prettyText
+        idPaths.forEach { path ->
+            updatedBundle = replaceId(bundle, path, updatedBundle)
+        }
+        return updatedBundle
+    }
+
+    /**
+     * Replaces the ID for a specific ID
+     */
+    private fun replaceId(bundle: Bundle, path: String, prettyText: String): String {
+        FhirPathUtils.evaluate(
+            null,
+            bundle,
+            bundle,
+            path
+        ).forEach { resourceId ->
+            val newIdentifier = getFakeValueForElementCall("UUID")
+            return prettyText.replace(resourceId.primitiveValue(), newIdentifier, true)
+        }
+        return prettyText
+    }
+
+    /**
+     * Gets a fake value for a given type
+     */
+    private fun getFakeValueForElementCall(dataType: String): String {
+        return CustomFhirPathFunctions().getFakeValueForElement(
+            mutableListOf(mutableListOf(StringType(dataType)))
+        )[0].primitiveValue()
+    }
+
+    /**
+     * Gets a fake value for a given type that requires geo data
+     */
+    private fun getFakeValueForElementCallUsingGeoData(dataType: String, state: String): String {
+        return CustomFhirPathFunctions().getFakeValueForElement(
+            mutableListOf(mutableListOf(StringType(dataType)), mutableListOf(StringType(state)))
+        )[0].primitiveValue()
+    }
+}

prime-router/src/main/kotlin/cli/main.kt

@@ -299,6 +299,7 @@ fun main(args: Array<String>) = RouterCli()
         ProcessHl7Commands(),
         ValidateTranslationSchemaCommand(),
         SyncTranslationSchemaCommand(),
-        ValidateYAMLCommand()
+        ValidateYAMLCommand(),
+        PIIRemovalCommands()
     ).context { terminal = Terminal(ansiLevel = AnsiLevel.TRUECOLOR) }
     .main(args)