[fern-api]

18.1.0 → 18.2.0

Added

• RequestOptions.Builder.addBodyProperty(String key, Object value) and .bodyProperties(Map<String, Object>) — inject arbitrary key-value pairs into the JSON or form-urlencoded request body at call time; properties override any same-named field already present in the body, and are sent as the entire body for endpoints that have none (multipart bodies are not supported).
• RequestOptions.getBodyProperties() — returns a snapshot Map of all body properties registered on the options object.
• RetryInterceptor.newAsyncCall(OkHttpClient, Request) — creates a non-blocking AsyncCall that schedules retries via a background daemon scheduler instead of sleeping inside an OkHttp dispatcher thread, so waiting retries no longer consume dispatcher slots (5 per host by default) and are cancelled immediately when cancel() is called.
• RetryInterceptor.AsyncCall — new public interface with enqueue(Callback) and cancel() returned by newAsyncCall.
• Stream.fromSseWithEventDiscrimination(...) — new static factory for SSE streams where certain union-variant events model the full SSE envelope ({"<discriminator>": event, "data": data}) while all other events are deserialized from the data payload with the discriminator injected.
• CreateOmopResponse.getQuantityTransformations() and .quantityTransformations(...) — new optional field that audits direct quantities on emitted drug_exposure rows, including derivations and omissions; entries use the response's vocabulary release.
• CreateOmopResponse.getRowsForReview() and .rowsForReview(...) — new optional index of otherwise shapeable clinical rows with uncertain source status or primary concept ID 0; tables now includes these previously-excluded rows, and consumers must filter by this index to exclude uncertain or unresolved rows from their load.
• CreateOmopResponse.getDeviceExposureContexts() and .deviceExposureContexts(...) — new optional field grouping timing, device evidence, and quantity explanation for each source record that produced device exposures.
• CreateOmopResponse.getSpecimenSourceContexts() and .specimenSourceContexts(...) — new optional field exposing source identities, availability status, and collection timing for emitted specimens, linked by request-local specimen_id.
• CreateOmopResponse.getMedicationDispenseSourceContexts() and .medicationDispenseSourceContexts(...) — new optional field linking dispensing status, timing, instructions, and references to each emitted dispensing row.
• DrugExposureRow.getQuantity() and Builder.quantity(...) — new optional Double field carrying the formulation-specific drug quantity from MedicationRequest dispense quantity, MedicationDispense quantity, MedicationAdministration dose, or Immunization dose quantity.
• MeasurementRow.getUnitSourceConceptId() and Builder.unitSourceConceptId(...) — new optional Long field with the OMOP source concept ID corresponding to Quantity.system/code; 0 for supplied but unmapped units, null for absent units.
• MappingEntry.getResolution() and Builder.resolution(...) — new optional MappingResolution field exposing structured mapping resolution detail, available on both the getter and the staged builder's _FinalStage.
• OmopTables.getDeviceExposure() and getSpecimen() — new optional table lists on OmopTables that surface DeviceExposureRow and SpecimenRow collections in FHIR-to-OMOP output, with matching builder setters.
• Summary.getRowsForReview() — new optional integer field reporting the count of rows flagged for review; each row is counted once regardless of how many retention reasons apply.
• VisitOccurrenceRow.getVisitSourceConceptId() — new optional OMOP source concept ID for the selected Encounter.class or Encounter.type coding, with matching builder setters.
• CreateMultiRequest.getSmallNote() / .smallNote(...) — new optional boolean builder field that bills the request at the lower small-note rate; when true, text must be at most 15,360 bytes (15 KiB) UTF-8 encoded.
• DeviceExposureContext, DeviceExposureLink, DeviceExposureEvidence, and DeviceExposureContextQuantityBasis — new FHIR-to-OMOP response types that expose device exposure row linkage, quantity basis, and original source evidence paths for each derived OMOP device exposure row.
• ExtractRequestConfigValidationMethod.SEMANTIC_MAPPING — new validation method constant and corresponding visitSemanticMapping() visitor method on ExtractRequestConfigValidationMethod, enabling semantic-mapping-based extraction validation.
• DeviceExposureRow — new OMOP CDM response type representing a device_exposure table row returned by the FHIR-to-OMOP conversion endpoint, with fields for concept IDs, start/end dates and datetimes, UDI (uniqueDeviceId), quantity, provider and visit linkage, device source value, and unit fields; includes a staged builder for type-safe construction.
• MappingResolution — new response type that describes the full vocabulary resolution outcome for an OMOP mapping entry, including getStatus(), getReasonCode(), getVia(), getPaths(), getTruncated(), and getSemanticMapping().
• MappingPath — new type representing a single mapping path to the selected OMOP concept, with getMappingStatus(), getSourceConceptId(), getSourceVocabulary(), getSourceCode(), and getCui().
• MappingResolutionStatus — new enum-like type with values RESOLVED, UNRESOLVED, DOMAIN_MISMATCH, and AMBIGUOUS indicating the overall vocabulary resolution outcome.
• MappingResolutionReasonCode — new enum-like type with machine-readable failure reasons (NO_SOURCE_CODE, NO_OMOP_SOURCE_CONCEPT, NO_STANDARD_MAP, AMBIGUOUS, DOMAIN_MISMATCH, UNSUPPORTED_SYSTEM, UNSUPPORTED_CODE) for unresolved mappings.
• MappingPathMappingStatus — new enum-like type with values ALREADY_STANDARD, MAPPED, and POLICY_MAPPED describing the outcome of an individual mapping path.
• MappingResolutionVia — new enum type (DIRECT, UMLS_BRIDGE) indicating how a concept mapping was resolved in FHIR-to-OMOP responses.
• MedicationDispenseSourceContext and MedicationDispenseSourceContextOmopTable — new response types carrying per-row FHIR source provenance (resource ID, full URL, OMOP table, OMOP ID, and raw source fields) for MedicationDispense resources.
• QuantityEvidence, QuantityDenominatorBasis, and QuantityDenominatorBasisKind — new types representing drug quantity transformation evidence, including drug concept class, dose form, strength, and denominator basis (PER_UNIT, QUANTIFIED_TOTAL, NOT_APPLICABLE).
• QuantityStrength — new fhir2omop type representing a drug ingredient's strength with a required ingredientConceptId and optional amount, numerator, and denominator quantity fields (value, unit, and denominator basis), all accessible via a staged builder.
• QuantityTransformation — new response model under com.phenoml.api.resources.fhir2omop.types that describes how a FHIR Quantity on a MedicationRequest was mapped to the OMOP drug_exposure.quantity field, including the source element path, original quantity object, linked drug_exposure_id, transformation outcome, applied policy, omission reason, supporting evidence, and numeric result with unit.
• QuantityTransformationOutcome — enum identifying whether a quantity was copied directly (DIRECT), calculated (DERIVED), or left unset (OMITTED).
• QuantityTransformationPolicy — enum identifying the formulation policy applied during derivation: FIXED_DOSE_FORM_COUNT or CLINICAL_INJECTION_INGREDIENT_AMOUNT.
• QuantityTransformationReason — new enum-like type with 14 named values (e.g. UNSUPPORTED_UNIT, DRUG_UNRESOLVED, AMBIGUOUS_DRUG_EVIDENCE) and a Visitor<T> interface for pattern-matching quantity transformation failure reasons.
• QuantityTransformationResourceType and QuantityTransformationSourcePath — new enum-like types identifying the FHIR resource kind (MedicationRequest, MedicationDispense, MedicationAdministration, Immunization) and the FHIR field path (quantity, doseQuantity, dosage.dose, dispenseRequest.quantity) involved in a quantity transformation.
• QuantityUnit — new staged-builder model exposing the resolved OMOP unit concept via getConceptId(), getCode(), and getVocabularyId().
• RowForReview — new staged-builder model linking a FHIR resource to an OMOP row (omopTable, omopId) with a list of RowForReviewReasonsItem reasons, an optional sourceFullUrl, and optional verbatim FHIR sourceStatuses.
• RowForReviewReasonsItem — new enum-like type with 7 named review reasons including CONDITION_VERIFICATION_UNCONFIRMED, ENCOUNTER_STATUS_UNKNOWN, and PRIMARY_CONCEPT_UNRESOLVED.
• SemanticMappingResult — new response type exposing whether semantic mapping selected a validated standard OMOP concept (status) and which OMOP vocabulary release was used (vocabVersion), with an optional reasonCode explaining unmapped outcomes.
• SemanticMappingResultStatus and SemanticMappingResultReasonCode — enums for the mapping outcome (MAPPED/UNMAPPED) and failure reason (MISSING_DESCRIPTION, NO_VALID_SUGGESTION, AMBIGUOUS, INVALID_TARGET), each with a Visitor for exhaustive handling.
• SpecimenCollectionTiming — new response type preserving the original FHIR specimen collection date/period fields (collectedDateTime, collectedPeriod, receivedTime) alongside selectedPath indicating which field populated specimen_date.
• SpecimenCollectionPeriod — companion type holding the raw collectedPeriod.start and collectedPeriod.end strings without precision completion.
• SpecimenIdentifier — new type with a required value and optional system for identifying a FHIR specimen resource.
• SpecimenRow — new OMOP CDM 5.4 Specimen domain type returned by the FHIR-to-OMOP pipeline, carrying specimen identity, material concept, collection date/time, quantity, unit, anatomic site, and source-value fields via a staged builder.

Changed

• MappingEntry Javadoc — mappingStatus, omopField, selected, and note descriptions updated to reflect expanded UNMAPPED semantics (domain mismatches, ambiguity, source-only entries) and entries without a corresponding row column.
• DrugExposureRow and MeasurementRow Javadoc — timing-source descriptions updated to include MedicationDispense and additional FHIR resources; drugTypeConceptId and unitConceptId gain inline documentation.

Fixed

• AsyncAgentClient — cancelling a returned CompletableFuture now propagates cancellation back to the underlying raw HTTP future, preventing orphaned in-flight requests.
• LogLevel.fromString() and LoggingInterceptor — use Locale.ROOT for case conversion, avoiding locale-sensitive mismatches on Turkish and other non-ASCII locales.

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