phenoml 17.2.0 → 17.3.0

package/dist/esm/api/resources/fhir2Omop/types/Summary.d.mts

@@ -0,0 +1,15 @@
+/**
+ * The request's data-quality headline: how the coded concepts split across
+ * resolution outcomes, and the share that was not already in a target
+ * standard vocabulary.
+ */
+export interface Summary {
+    /** Codings already a standard OMOP concept. */
+    codes_already_standard?: number | undefined;
+    /** Codings mapped or suggested to a standard concept (MAPPED or UNCHECKED). */
+    codes_normalized?: number | undefined;
+    /** Codings with no standard concept found. */
+    codes_unmapped?: number | undefined;
+    /** Share of coded concepts not already standard ((normalized + unmapped) / total). */
+    off_vocab_rate?: number | undefined;
+}

package/dist/esm/api/resources/fhir2Omop/types/index.d.mts

@@ -2,11 +2,11 @@ export * from "./ConditionOccurrenceRow.mjs";
 export * from "./CreateOmopResponse.mjs";
 export * from "./DroppedResource.mjs";
 export * from "./DrugExposureRow.mjs";
-export * from "./MappingReportEntry.mjs";
+export * from "./MappingEntry.mjs";
 export * from "./MeasurementRow.mjs";
 export * from "./ObservationRow.mjs";
 export * from "./OmopTables.mjs";
 export * from "./PersonRow.mjs";
 export * from "./ProcedureOccurrenceRow.mjs";
-export * from "./ScanSummary.mjs";
+export * from "./Summary.mjs";
 export * from "./VisitOccurrenceRow.mjs";

package/dist/esm/api/resources/fhir2Omop/types/index.mjs

@@ -2,11 +2,11 @@ export * from "./ConditionOccurrenceRow.mjs";
 export * from "./CreateOmopResponse.mjs";
 export * from "./DroppedResource.mjs";
 export * from "./DrugExposureRow.mjs";
-export * from "./MappingReportEntry.mjs";
+export * from "./MappingEntry.mjs";
 export * from "./MeasurementRow.mjs";
 export * from "./ObservationRow.mjs";
 export * from "./OmopTables.mjs";
 export * from "./PersonRow.mjs";
 export * from "./ProcedureOccurrenceRow.mjs";
-export * from "./ScanSummary.mjs";
+export * from "./Summary.mjs";
 export * from "./VisitOccurrenceRow.mjs";

package/dist/esm/core/fetcher/signals.mjs

@@ -10,11 +10,19 @@ export function anySignal(...args) {
     for (const signal of signals) {
         if (signal.aborted) {
             controller.abort(signal === null || signal === void 0 ? void 0 : signal.reason);
-            break;
+            return controller.signal;
         }
         signal.addEventListener("abort", () => controller.abort(signal === null || signal === void 0 ? void 0 : signal.reason), {
             signal: controller.signal,
         });
+        // Re-check after adding listener: the signal may have aborted
+        // between the initial `signal.aborted` check and the `addEventListener`
+        // call above. If it did, the abort event was already dispatched and
+        // the listener will never fire — we must manually abort.
+        if (signal.aborted) {
+            controller.abort(signal === null || signal === void 0 ? void 0 : signal.reason);
+            return controller.signal;
+        }
     }
     return controller.signal;
 }

package/dist/esm/version.d.mts

@@ -1 +1 @@
-export declare const SDK_VERSION = "17.2.0";
+export declare const SDK_VERSION = "17.3.0";

package/dist/esm/version.mjs

@@ -1 +1 @@
-export const SDK_VERSION = "17.2.0";
+export const SDK_VERSION = "17.3.0";

package/openapi/openapi.json

@@ -2,7 +2,7 @@
   "openapi": "3.0.3",
   "info": {
     "title": "Phenoml API",
-    "version": "f96459701356d9f1fe1acbeab0f6f2eccc498046"
+    "version": "5084e3096e5bd89bf2e86ea44d96e3407f6f5c6b"
   },
   "x-services": [
     {
@@ -3021,7 +3021,7 @@
       "post": {
         "operationId": "fhir2omop_create",
         "summary": "Map FHIR resources to OMOP CDM v5.4",
-        "description": "Shapes a FHIR R4 resource or Bundle into OMOP Common Data Model v5.4 rows\n(person, visit_occurrence, condition_occurrence, drug_exposure,\nprocedure_occurrence, measurement, observation).\n\n**Two resolution modes, reported in `mode`.** `mode` reflects which\nresolver is wired, not the path an individual coding took. With a\nconcept-resolver configured (the default), `mode` is `\"resolved\"` and the\nresource's primary clinical coding is resolved to a real OMOP `concept_id`;\nwith no resolver configured, `mode` is `\"structural\"` and every clinical\nand source `concept_id` is `0`. In `\"resolved\"` mode individual codings can\nstill land at `concept_id` `0` without changing the mode: a coding the\nservice finds no match for is `UNMAPPED`, and a coding that fell back to the\nstructural tier (the resolver was briefly unavailable, or the resource was\ntext-only) is surfaced in `scan_summary` (`concept_resolver_note`,\n`construe_resolutions`). A `concept_id` of `0` is \"no matching concept\" per\nOMOP semantics, deliberately not omitted. Only the primary clinical coding\nis resolved \u2014 `gender`/`race`/`ethnicity`/`visit`/`value`/`unit`\n`concept_id`s are always `0`.\n\nIn every mode each `*_source_value` carries the verbatim FHIR coding\n(`system#code`), `*_type_concept_id` is set to `32817` (EHR), and the\nresponse `report` lists one Usagi-shaped entry per source coding describing\nhow it resolved (`ALREADY_STANDARD`, `MAPPED`, an `UNCHECKED` suggestion,\nor `UNMAPPED`).\n\nMedication codes are resolved whether they appear inline\n(`medicationCodeableConcept`) or via a `medicationReference` to a contained,\nrelative (`Type/id`), or bundle-entry (`urn:uuid`) `Medication` resource.\nResources that cannot be shaped into a row \u2014 a medication with no usable\ncode, resolvable reference, or display, or any clinical resource whose\nsubject/patient reference cannot be tied to a person \u2014 are reported under\n`scan_summary.dropped_resources` rather than emitted as blank rows. The\nbundle must contain at least one Patient resource.\n",
+        "description": "Maps a FHIR R4 resource or Bundle into OMOP Common Data Model v5.4 rows\n(person, visit_occurrence, condition_occurrence, drug_exposure,\nprocedure_occurrence, measurement, observation).\n\nEach resource's primary clinical coding is resolved to a standard OMOP\n`concept_id`. Alongside the OMOP rows grouped by table (`tables`), the\nresponse carries `mappings` (how each source coding resolved, linked back\nto the row it produced), `dropped` (resources that could not be shaped\ninto a row), `vocab_version` (the OMOP vocabulary release codes were\nresolved against), and a small `summary` of the resolution outcomes.\n\nA `concept_id` of `0` means \"no matching standard concept\" (OMOP\nsemantics) and is reported, not omitted \u2014 a coding with no match is\n`UNMAPPED`. Only the primary clinical coding is resolved;\n`gender`/`race`/`ethnicity`/`visit`/`value`/`unit` `concept_id`s are\nalways `0`. Each `*_source_value` carries the verbatim FHIR coding\n(`system#code`), and `*_type_concept_id` is set to `32817` (EHR).\n\nMedication codes are resolved whether they appear inline\n(`medicationCodeableConcept`) or via a `medicationReference` to a contained,\nrelative (`Type/id`), or bundle-entry (`urn:uuid`) `Medication` resource.\nResources that cannot be shaped into a row \u2014 a medication with no usable\ncode, resolvable reference, or display, or any clinical resource whose\nsubject/patient reference cannot be tied to a person \u2014 are reported under\n`dropped` rather than emitted as blank rows. The\nbundle must contain at least one Patient resource.\n",
         "requestBody": {
           "required": true,
           "content": {
@@ -3111,13 +3111,12 @@
                   "$ref": "#/components/schemas/fhir2omop_CreateOmopResponse"
                 },
                 "examples": {
-                  "resolved_mapping": {
-                    "summary": "Resolved mapping result (default)",
-                    "description": "Same bundle with `concept_id`s filled by the concept-resolver\nservice. Both source codes are already standard, so each carries\nits own OMOP `concept_id` with `ALREADY_STANDARD` status;\n`target_code` is omitted because the service returns the standard\nconcept's id, name, and vocabulary rather than its `concept_code`.\nIllustrative `concept_id` values.\n",
+                  "mapping_result": {
+                    "summary": "Mapping result",
+                    "description": "The example bundle mapped to OMOP. Both source codes are already\nstandard, so each clinical row carries its own OMOP `concept_id`\nwith `ALREADY_STANDARD` status. `target_code` is omitted for a\nresolved concept \u2014 it is identified by `target_vocabulary` and\n`target_name` (and the row's `*_concept_id`). Illustrative\n`concept_id` values.\n",
                     "value": {
                       "success": true,
-                      "message": "FHIR resources mapped to OMOP CDM v5.4 with vocabulary concept resolution",
-                      "mode": "resolved",
+                      "message": "FHIR resources mapped to OMOP CDM v5.4",
                       "tables": {
                         "person": [
                           {
@@ -3158,11 +3157,12 @@
                           }
                         ]
                       },
-                      "report": [
+                      "mappings": [
                         {
                           "resource_type": "Condition",
                           "resource_id": "condition-1",
                           "omop_table": "condition_occurrence",
+                          "omop_id": 1,
                           "source_system": "http://snomed.info/sct",
                           "source_code": "44054006",
                           "source_name": "Type 2 diabetes mellitus",
@@ -3174,6 +3174,7 @@
                           "resource_type": "MedicationRequest",
                           "resource_id": "medreq-1",
                           "omop_table": "drug_exposure",
+                          "omop_id": 1,
                           "source_system": "http://www.nlm.nih.gov/research/umls/rxnorm",
                           "source_code": "860975",
                           "source_name": "metformin hydrochloride 500 MG",
@@ -3182,118 +3183,8 @@
                           "mapping_status": "ALREADY_STANDARD"
                         }
                       ],
-                      "scan_summary": {
-                        "total_resources": 3,
-                        "resource_counts": {
-                          "Patient": 1,
-                          "Condition": 1,
-                          "MedicationRequest": 1
-                        },
-                        "tables_populated": {
-                          "person": 1,
-                          "condition_occurrence": 1,
-                          "drug_exposure": 1
-                        },
-                        "coding_systems": {
-                          "http://snomed.info/sct": 1,
-                          "http://www.nlm.nih.gov/research/umls/rxnorm": 1
-                        },
-                        "codes_already_standard": 2,
-                        "codes_normalized": 0,
-                        "codes_unmapped": 0,
-                        "off_vocab_rate": 0,
-                        "resolved_vocab_version": "v20240229"
-                      }
-                    }
-                  },
-                  "structural_mapping": {
-                    "summary": "Structural mapping result (fallback / no resolver configured)",
-                    "value": {
-                      "success": true,
-                      "message": "FHIR resources mapped to OMOP CDM v5.4 (structural; concept_ids pending vocabulary crosswalk)",
-                      "mode": "structural",
-                      "tables": {
-                        "person": [
-                          {
-                            "person_id": 1,
-                            "gender_concept_id": 0,
-                            "year_of_birth": 1985,
-                            "month_of_birth": 7,
-                            "day_of_birth": 22,
-                            "birth_datetime": "1985-07-22",
-                            "race_concept_id": 0,
-                            "ethnicity_concept_id": 0,
-                            "person_source_value": "patient-1",
-                            "gender_source_value": "female"
-                          }
-                        ],
-                        "condition_occurrence": [
-                          {
-                            "condition_occurrence_id": 1,
-                            "person_id": 1,
-                            "condition_concept_id": 0,
-                            "condition_start_date": "2024-01-15",
-                            "condition_start_datetime": "2024-01-15",
-                            "condition_type_concept_id": 32817,
-                            "condition_source_value": "http://snomed.info/sct#44054006",
-                            "condition_source_concept_id": 0
-                          }
-                        ],
-                        "drug_exposure": [
-                          {
-                            "drug_exposure_id": 1,
-                            "person_id": 1,
-                            "drug_concept_id": 0,
-                            "drug_exposure_start_date": "2024-01-16",
-                            "drug_exposure_start_datetime": "2024-01-16",
-                            "drug_type_concept_id": 32817,
-                            "drug_source_value": "http://www.nlm.nih.gov/research/umls/rxnorm#860975",
-                            "drug_source_concept_id": 0
-                          }
-                        ]
-                      },
-                      "report": [
-                        {
-                          "resource_type": "Condition",
-                          "resource_id": "condition-1",
-                          "omop_table": "condition_occurrence",
-                          "source_system": "http://snomed.info/sct",
-                          "source_code": "44054006",
-                          "source_name": "Type 2 diabetes mellitus",
-                          "target_vocabulary": "SNOMED",
-                          "target_code": "44054006",
-                          "target_name": "Type 2 diabetes mellitus",
-                          "mapping_status": "ALREADY_STANDARD"
-                        },
-                        {
-                          "resource_type": "MedicationRequest",
-                          "resource_id": "medreq-1",
-                          "omop_table": "drug_exposure",
-                          "source_system": "http://www.nlm.nih.gov/research/umls/rxnorm",
-                          "source_code": "860975",
-                          "source_name": "metformin hydrochloride 500 MG",
-                          "target_vocabulary": "RXNORM",
-                          "target_code": "860975",
-                          "target_name": "metformin hydrochloride 500 MG",
-                          "mapping_status": "ALREADY_STANDARD"
-                        }
-                      ],
-                      "scan_summary": {
-                        "total_resources": 3,
-                        "resource_counts": {
-                          "Patient": 1,
-                          "Condition": 1,
-                          "MedicationRequest": 1
-                        },
-                        "tables_populated": {
-                          "person": 1,
-                          "condition_occurrence": 1,
-                          "drug_exposure": 1
-                        },
-                        "coding_systems": {
-                          "http://snomed.info/sct": 1,
-                          "http://www.nlm.nih.gov/research/umls/rxnorm": 1
-                        },
+                      "vocab_version": "v20240229",
+                      "summary": {
                         "codes_already_standard": 2,
                         "codes_normalized": 0,
                         "codes_unmapped": 0,
@@ -3306,7 +3197,7 @@
             }
           },
           "400": {
-            "description": "Bad request - invalid input. Possible reasons:\n- Invalid FHIR input (missing or non-Bundle/non-resource payload)\n- No Patient resource found (OMOP requires at least one person)\n",
+            "description": "Bad request - invalid input. Possible reasons:\n- Missing or malformed request body (no `fhir_resources`)\n- Invalid FHIR input (non-Bundle/non-resource payload)\n- No Patient resource found (OMOP requires at least one person)\n",
             "content": {
               "application/json": {
                 "schema": {
@@ -3320,6 +3211,16 @@
           },
           "500": {
             "description": "Internal server error"
+          },
+          "503": {
+            "description": "Service unavailable due to a server configuration error. No rows are\nreturned.\n",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/fhir2omop_CreateOmopResponse"
+                }
+              }
+            }
           }
         },
         "security": [
@@ -8654,22 +8555,29 @@
           "message": {
             "type": "string"
           },
-          "mode": {
-            "type": "string",
-            "description": "Resolution mode. `resolved` (default) means clinical `concept_id`s were\nfilled by the concept-resolver service; `structural` means no resolver\nwas configured, so all clinical `concept_id`s are `0`. Reflects which\nresolver is wired, not the path an individual coding took \u2014 per-coding\ndegradation is surfaced in `scan_summary`, not the mode.\n"
-          },
           "tables": {
             "$ref": "#/components/schemas/fhir2omop_OmopTables"
           },
-          "report": {
+          "mappings": {
+            "type": "array",
+            "description": "One entry per source coding (or one entry for a text-only resource with no coding), describing how it resolved and linking back to the row it produced.",
+            "items": {
+              "$ref": "#/components/schemas/fhir2omop_MappingEntry"
+            }
+          },
+          "dropped": {
             "type": "array",
-            "description": "One Usagi-shaped entry per source coding routed through concept resolution.",
+            "description": "Resources that could not be shaped into an OMOP row (rather than emitted as blank rows).",
             "items": {
-              "$ref": "#/components/schemas/fhir2omop_MappingReportEntry"
+              "$ref": "#/components/schemas/fhir2omop_DroppedResource"
             }
           },
-          "scan_summary": {
-            "$ref": "#/components/schemas/fhir2omop_ScanSummary"
+          "vocab_version": {
+            "type": "string",
+            "description": "The OMOP vocabulary release the clinical codes were resolved against\n(e.g. \"v20240229\"), for reproducibility. Present when at least one\ncoded concept was resolved.\n"
+          },
+          "summary": {
+            "$ref": "#/components/schemas/fhir2omop_Summary"
           }
         }
       },
@@ -9034,9 +8942,9 @@
           }
         }
       },
-      "fhir2omop_MappingReportEntry": {
+      "fhir2omop_MappingEntry": {
         "type": "object",
-        "description": "One source_to_concept_map-style mapping suggestion (Usagi-shaped).",
+        "description": "How one source coding (or a text-only resource's free text) resolved to an OMOP standard concept.",
         "properties": {
           "resource_type": {
             "type": "string"
@@ -9047,6 +8955,11 @@
           "omop_table": {
             "type": "string"
           },
+          "omop_id": {
+            "type": "integer",
+            "format": "int64",
+            "description": "The id of the OMOP row this coding produced (e.g. `condition_occurrence_id`),\nwithin `omop_table`. A resource with multiple codings yields one entry\nper coding, all sharing this id.\n"
+          },
           "source_system": {
             "type": "string"
           },
@@ -9061,83 +8974,40 @@
           },
           "target_code": {
             "type": "string",
-            "description": "Standard concept code. Set when a coding is matched by the structural\n(construe) tier \u2014 an already-standard code taken verbatim, or a\nconstrue-suggested code \u2014 which is every match in structural mode and,\nin resolved mode, codings for text-only resources or ones that fell back\nwhen the resolver was unavailable. Omitted for codings resolved directly\nby the concept-resolver service, which returns the standard concept's\nid, name, and vocabulary but not its `concept_code`.\n"
+            "description": "The standard concept's code, when present. Populated only for an\n`UNCHECKED` suggestion (where the API normalized a text-only resource\nto a suggested code); omitted for codings resolved through concept\nresolution (`ALREADY_STANDARD` / `MAPPED` / `UNMAPPED`), which are\nidentified by `target_vocabulary`, `target_name`, and the row's\n`*_concept_id` rather than by code.\n"
           },
           "target_name": {
             "type": "string"
           },
           "mapping_status": {
             "type": "string",
-            "description": "ALREADY_STANDARD (source already in the target standard vocabulary),\nMAPPED (resolved to a standard concept via the OMOP \"Maps to\" crosswalk\nor UMLS-CUI bridge; resolved mode only), UNCHECKED (an unreviewed\nconstrue suggestion; structural / fallback only), or UNMAPPED (no\ncandidate found).\n"
+            "description": "ALREADY_STANDARD (source coding is already a standard OMOP concept),\nMAPPED (source coding was mapped to a standard concept), UNCHECKED (a\nstandard code was suggested \u2014 e.g. for a text-only resource \u2014 but not\nverified against the OMOP vocabulary, so `concept_id` stays `0`), or\nUNMAPPED (no standard concept found).\n"
           },
           "note": {
             "type": "string"
           }
         }
       },
-      "fhir2omop_ScanSummary": {
+      "fhir2omop_Summary": {
         "type": "object",
-        "description": "White Rabbit-style aggregate profile of the mapping request.",
+        "description": "The request's data-quality headline: how the coded concepts split across\nresolution outcomes, and the share that was not already in a target\nstandard vocabulary.\n",
         "properties": {
-          "total_resources": {
-            "type": "integer"
-          },
-          "resource_counts": {
-            "type": "object",
-            "additionalProperties": {
-              "type": "integer"
-            }
-          },
-          "tables_populated": {
-            "type": "object",
-            "additionalProperties": {
-              "type": "integer"
-            }
-          },
-          "coding_systems": {
-            "type": "object",
-            "additionalProperties": {
-              "type": "integer"
-            }
-          },
           "codes_already_standard": {
-            "type": "integer"
+            "type": "integer",
+            "description": "Codings already a standard OMOP concept."
           },
           "codes_normalized": {
-            "type": "integer"
+            "type": "integer",
+            "description": "Codings mapped or suggested to a standard concept (MAPPED or UNCHECKED)."
           },
           "codes_unmapped": {
-            "type": "integer"
+            "type": "integer",
+            "description": "Codings with no standard concept found."
           },
           "off_vocab_rate": {
             "type": "number",
-            "format": "double"
-          },
-          "dropped_resources": {
-            "type": "array",
-            "items": {
-              "$ref": "#/components/schemas/fhir2omop_DroppedResource"
-            }
-          },
-          "resolved_vocab_version": {
-            "type": "string",
-            "description": "OMOP vocabulary release the resolver mapped against (e.g. \"v20240229\").\nResolved mode only; empty when no coded concept reached the service.\n"
-          },
-          "concept_resolver_note": {
-            "type": "string",
-            "description": "Set when concept resolution was degraded \u2014 the resolver was unavailable\nfor one or more codings, whose `concept_id`s fell back to the structural\n(construe) tier. Empty when resolution was clean.\n"
-          },
-          "concepts_bridged": {
-            "type": "integer",
-            "description": "Count of `concept_id`s chosen via the lower-confidence UMLS-CUI bridge\n(no direct OMOP crosswalk existed). Resolved mode only.\n"
-          },
-          "concept_candidates_truncated": {
-            "type": "integer",
-            "description": "Count of codings whose candidate list the resolver capped, so the best\nconcept may not have been among those returned.\n"
-          },
-          "construe_resolutions": {
-            "type": "integer",
-            "description": "Count of codings resolved via the construe ML extractor \u2014 the text-only\nor availability fallback path. A non-zero value bills the construe tier.\n"
+            "format": "double",
+            "description": "Share of coded concepts not already standard ((normalized + unmapped) / total)."
           }
         }
       },

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "phenoml",
-    "version": "17.2.0",
+    "version": "17.3.0",
     "private": false,
     "repository": {
         "type": "git",

package/reference.md

@@ -2673,30 +2673,23 @@ The ID of the FHIR provider to use. Can be either:
 <dl>
 <dd>
 
-Shapes a FHIR R4 resource or Bundle into OMOP Common Data Model v5.4 rows
+Maps a FHIR R4 resource or Bundle into OMOP Common Data Model v5.4 rows
 (person, visit_occurrence, condition_occurrence, drug_exposure,
 procedure_occurrence, measurement, observation).
 
-**Two resolution modes, reported in `mode`.** `mode` reflects which
-resolver is wired, not the path an individual coding took. With a
-concept-resolver configured (the default), `mode` is `"resolved"` and the
-resource's primary clinical coding is resolved to a real OMOP `concept_id`;
-with no resolver configured, `mode` is `"structural"` and every clinical
-and source `concept_id` is `0`. In `"resolved"` mode individual codings can
-still land at `concept_id` `0` without changing the mode: a coding the
-service finds no match for is `UNMAPPED`, and a coding that fell back to the
-structural tier (the resolver was briefly unavailable, or the resource was
-text-only) is surfaced in `scan_summary` (`concept_resolver_note`,
-`construe_resolutions`). A `concept_id` of `0` is "no matching concept" per
-OMOP semantics, deliberately not omitted. Only the primary clinical coding
-is resolved — `gender`/`race`/`ethnicity`/`visit`/`value`/`unit`
-`concept_id`s are always `0`.
-
-In every mode each `*_source_value` carries the verbatim FHIR coding
-(`system#code`), `*_type_concept_id` is set to `32817` (EHR), and the
-response `report` lists one Usagi-shaped entry per source coding describing
-how it resolved (`ALREADY_STANDARD`, `MAPPED`, an `UNCHECKED` suggestion,
-or `UNMAPPED`).
+Each resource's primary clinical coding is resolved to a standard OMOP
+`concept_id`. Alongside the OMOP rows grouped by table (`tables`), the
+response carries `mappings` (how each source coding resolved, linked back
+to the row it produced), `dropped` (resources that could not be shaped
+into a row), `vocab_version` (the OMOP vocabulary release codes were
+resolved against), and a small `summary` of the resolution outcomes.
+
+A `concept_id` of `0` means "no matching standard concept" (OMOP
+semantics) and is reported, not omitted — a coding with no match is
+`UNMAPPED`. Only the primary clinical coding is resolved;
+`gender`/`race`/`ethnicity`/`visit`/`value`/`unit` `concept_id`s are
+always `0`. Each `*_source_value` carries the verbatim FHIR coding
+(`system#code`), and `*_type_concept_id` is set to `32817` (EHR).
 
 Medication codes are resolved whether they appear inline
 (`medicationCodeableConcept`) or via a `medicationReference` to a contained,
@@ -2704,7 +2697,7 @@ relative (`Type/id`), or bundle-entry (`urn:uuid`) `Medication` resource.
 Resources that cannot be shaped into a row — a medication with no usable
 code, resolvable reference, or display, or any clinical resource whose
 subject/patient reference cannot be tied to a person — are reported under
-`scan_summary.dropped_resources` rather than emitted as blank rows. The
+`dropped` rather than emitted as blank rows. The
 bundle must contain at least one Patient resource.
 </dd>
 </dl>

package/dist/cjs/api/resources/fhir2Omop/types/MappingReportEntry.d.ts

@@ -1,32 +0,0 @@
-/**
- * One source_to_concept_map-style mapping suggestion (Usagi-shaped).
- */
-export interface MappingReportEntry {
-    resource_type?: string | undefined;
-    resource_id?: string | undefined;
-    omop_table?: string | undefined;
-    source_system?: string | undefined;
-    source_code?: string | undefined;
-    source_name?: string | undefined;
-    target_vocabulary?: string | undefined;
-    /**
-     * Standard concept code. Set when a coding is matched by the structural
-     * (construe) tier — an already-standard code taken verbatim, or a
-     * construe-suggested code — which is every match in structural mode and,
-     * in resolved mode, codings for text-only resources or ones that fell back
-     * when the resolver was unavailable. Omitted for codings resolved directly
-     * by the concept-resolver service, which returns the standard concept's
-     * id, name, and vocabulary but not its `concept_code`.
-     */
-    target_code?: string | undefined;
-    target_name?: string | undefined;
-    /**
-     * ALREADY_STANDARD (source already in the target standard vocabulary),
-     * MAPPED (resolved to a standard concept via the OMOP "Maps to" crosswalk
-     * or UMLS-CUI bridge; resolved mode only), UNCHECKED (an unreviewed
-     * construe suggestion; structural / fallback only), or UNMAPPED (no
-     * candidate found).
-     */
-    mapping_status?: string | undefined;
-    note?: string | undefined;
-}

package/dist/cjs/api/resources/fhir2Omop/types/ScanSummary.d.ts

@@ -1,41 +0,0 @@
-import type * as phenoml from "../../../index.js";
-/**
- * White Rabbit-style aggregate profile of the mapping request.
- */
-export interface ScanSummary {
-    total_resources?: number | undefined;
-    resource_counts?: Record<string, number> | undefined;
-    tables_populated?: Record<string, number> | undefined;
-    coding_systems?: Record<string, number> | undefined;
-    codes_already_standard?: number | undefined;
-    codes_normalized?: number | undefined;
-    codes_unmapped?: number | undefined;
-    off_vocab_rate?: number | undefined;
-    dropped_resources?: phenoml.fhir2Omop.DroppedResource[] | undefined;
-    /**
-     * OMOP vocabulary release the resolver mapped against (e.g. "v20240229").
-     * Resolved mode only; empty when no coded concept reached the service.
-     */
-    resolved_vocab_version?: string | undefined;
-    /**
-     * Set when concept resolution was degraded — the resolver was unavailable
-     * for one or more codings, whose `concept_id`s fell back to the structural
-     * (construe) tier. Empty when resolution was clean.
-     */
-    concept_resolver_note?: string | undefined;
-    /**
-     * Count of `concept_id`s chosen via the lower-confidence UMLS-CUI bridge
-     * (no direct OMOP crosswalk existed). Resolved mode only.
-     */
-    concepts_bridged?: number | undefined;
-    /**
-     * Count of codings whose candidate list the resolver capped, so the best
-     * concept may not have been among those returned.
-     */
-    concept_candidates_truncated?: number | undefined;
-    /**
-     * Count of codings resolved via the construe ML extractor — the text-only
-     * or availability fallback path. A non-zero value bills the construe tier.
-     */
-    construe_resolutions?: number | undefined;
-}

package/dist/esm/api/resources/fhir2Omop/types/MappingReportEntry.d.mts

@@ -1,32 +0,0 @@
-/**
- * One source_to_concept_map-style mapping suggestion (Usagi-shaped).
- */
-export interface MappingReportEntry {
-    resource_type?: string | undefined;
-    resource_id?: string | undefined;
-    omop_table?: string | undefined;
-    source_system?: string | undefined;
-    source_code?: string | undefined;
-    source_name?: string | undefined;
-    target_vocabulary?: string | undefined;
-    /**
-     * Standard concept code. Set when a coding is matched by the structural
-     * (construe) tier — an already-standard code taken verbatim, or a
-     * construe-suggested code — which is every match in structural mode and,
-     * in resolved mode, codings for text-only resources or ones that fell back
-     * when the resolver was unavailable. Omitted for codings resolved directly
-     * by the concept-resolver service, which returns the standard concept's
-     * id, name, and vocabulary but not its `concept_code`.
-     */
-    target_code?: string | undefined;
-    target_name?: string | undefined;
-    /**
-     * ALREADY_STANDARD (source already in the target standard vocabulary),
-     * MAPPED (resolved to a standard concept via the OMOP "Maps to" crosswalk
-     * or UMLS-CUI bridge; resolved mode only), UNCHECKED (an unreviewed
-     * construe suggestion; structural / fallback only), or UNMAPPED (no
-     * candidate found).
-     */
-    mapping_status?: string | undefined;
-    note?: string | undefined;
-}