feat(OGC-1054): make analyzer recognition profile-owned

.github/workflows/test.yml

@@ -22,7 +22,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: DIGI-UW/analyzer-mock-server
-          ref: 504ffec81a5b93f6be91231051e8fe0720f61eb1
+          ref: b56fc7f8b93b0912894ffcebaeb3bde61e32864b
           path: analyzer-mock-server
 
       - name: Set up JDK 21

README.md

@@ -113,6 +113,7 @@ Runtime configuration is read from `configuration.yml` (mounted into container a
 | `org.itech.ahb.forward-http-server.max-attempts` | Outbound retry attempts | 3 |
 | `org.itech.ahb.forward-http-server.backoff-ms` | Initial outbound retry backoff in ms | 1000 |
 | **ASTM TCP** | | |
+| `org.itech.ahb.astm.enabled` | Enable ASTM TCP listeners | true |
 | `org.itech.ahb.listen-astm-server.port` | ASTM LIS1-A listen port | 12001 |
 | `org.itech.ahb.listen-astm-e1381-95-server.port` | E1381-95 listen port | 12011 |
 | **MLLP (HL7)** | | |

configuration.yml

@@ -68,7 +68,7 @@ bridge:
 
   # File watcher configuration (M4)
   # Runtime ownership note (014 remediation): Bridge is the active FILE watcher owner.
-  # OpenELIS app-side poller is fallback-only and disabled by default.
+  # OpenELIS configures and registers FILE analyzers but does not watch directories.
   file:
     enabled: false  # Bootstrap default; watcher is activated by FILE registration lifecycle during remediation
     watchDirectories:
@@ -113,6 +113,9 @@ org:
         max-attempts: 3
         backoff-ms: 1000
 
+      astm:
+        enabled: true
+
       # ASTM LIS1-A Server - Listens for ASTM messages from analyzers
       listen-astm-server:
         port: 12001

contracts/analyzer/v1/analyzer-profile.schema.json

@@ -83,6 +83,12 @@
         ]
       }
     },
+    "result_value_order": {
+      "type": "array",
+      "minItems": 1,
+      "uniqueItems": true,
+      "items": { "enum": ["result", "ctValue", "interpretation"] }
+    },
     "sheet_detection": { "$ref": "#/$defs/sheetDetection" },
     "default_test_mappings": {
       "type": "array",
@@ -125,7 +131,7 @@
             "minItems": 1,
             "items": { "$ref": "#/$defs/testMapping" }
           },
-          "configDefaults": { "$ref": "#/$defs/socketDefaults" },
+          "configDefaults": { "$ref": "#/$defs/astmSocketDefaults" },
           "controlResultRecognition": {
             "$ref": "#/$defs/astmControlResultRecognition"
           }
@@ -385,6 +391,51 @@
         "transforms": { "type": "object" }
       }
     },
+    "astmSocketDefaults": {
+      "allOf": [
+        { "$ref": "#/$defs/socketDefaults" },
+        {
+          "required": ["extractionOverrides"],
+          "properties": {
+            "extractionOverrides": {
+              "$ref": "#/$defs/astmExtractionOverrides"
+            }
+          }
+        }
+      ]
+    },
+    "astmExtractionOverrides": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["resultRecordSelection"],
+      "properties": {
+        "resultRecordSelection": {
+          "$ref": "#/$defs/astmResultRecordSelection"
+        }
+      }
+    },
+    "astmResultRecordSelection": {
+      "oneOf": [
+        {
+          "type": "object",
+          "additionalProperties": false,
+          "required": ["mode"],
+          "properties": { "mode": { "const": "ALL" } }
+        },
+        {
+          "type": "object",
+          "additionalProperties": false,
+          "required": ["mode", "targetField"],
+          "properties": {
+            "mode": { "const": "FIELD_NON_BLANK" },
+            "targetField": {
+              "type": "string",
+              "pattern": "^R\\.[1-9][0-9]*\\.[1-9][0-9]*$"
+            }
+          }
+        }
+      ]
+    },
     "fileDefaults": {
       "type": "object",
       "additionalProperties": false,

contracts/analyzer/v1/fixtures/analyzer-profile-astm.json

@@ -76,7 +76,12 @@
     "connectionRole": "SERVER",
     "transport": "TCP/IP",
     "aggregationMode": "PER_MESSAGE",
-    "extractionOverrides": {},
+    "extractionOverrides": {
+      "resultRecordSelection": {
+        "mode": "FIELD_NON_BLANK",
+        "targetField": "R.3.5"
+      }
+    },
     "flagMappings": {},
     "transforms": {}
   },
@@ -139,7 +144,7 @@
   },
   "catalog": {
     "revision": 1,
-    "revisionFingerprint": "sha256:5184c52a44ec58932116fb3c4e9495b6cd8f05e4e84916f183f57b428a24e4ee",
+    "revisionFingerprint": "sha256:c2168ff7438aaea72eb4dcd646e2348601899b4b401b3c235fae07b5804081b2",
     "recognitionFingerprint": "sha256:68a4cf6c695d3a23662a7a5dc97983bbc78e38726f932517d09238d47aad701e",
     "source": "SHIPPED",
     "status": "ACTIVE",

contracts/analyzer/v1/fixtures/analyzer-profile-file.json

@@ -33,6 +33,7 @@
     "testCode": "testCode",
     "WellPosition": "position"
   },
+  "result_value_order": ["result", "interpretation"],
   "default_test_mappings": [
     {
       "test_code": "VIH-1",
@@ -94,7 +95,7 @@
   },
   "catalog": {
     "revision": 1,
-    "revisionFingerprint": "sha256:8d099084227b7de083a6f8f0511234c8f09540534182a380060fe921a7f28c21",
+    "revisionFingerprint": "sha256:a39955225875ee8cc4ae2a5a0c587acd5c9e376749485ef48ef1eca2cefcf770",
     "recognitionFingerprint": "sha256:5c0de42e1135b772b23e4c1ea04b0162b30fe36fc08ecef76a70108ba031be26",
     "source": "SHIPPED",
     "status": "ACTIVE",

contracts/analyzer/v1/fixtures/analyzer-profile-quantstudio.json

@@ -30,6 +30,7 @@
     "Well Position": "position",
     "Task": "qcTask"
   },
+  "result_value_order": ["result", "ctValue"],
   "sheet_detection": {
     "strategy": "header_scan",
     "preferred_sheet_names": ["Results"],
@@ -100,7 +101,7 @@
   },
   "catalog": {
     "revision": 1,
-    "revisionFingerprint": "sha256:b940cb5cc7191a44570a87326e7e5c2054f4ac6df42cdf653ae113b9df143e6e",
+    "revisionFingerprint": "sha256:8b0d72f2b60dbfa2b025599a796a83c89fe2fcca3d329fbde3400f7a1434896e",
     "recognitionFingerprint": "sha256:e5c668abfd8b64220efeff01dd57682dcbd883f2652d68d187505bbd4ac707ab",
     "source": "SHIPPED",
     "status": "ACTIVE",

contracts/analyzer/v1/fixtures/profile-catalog-response.json

@@ -38,6 +38,7 @@
           "testCode": "testCode",
           "WellPosition": "position"
         },
+        "result_value_order": ["result", "interpretation"],
         "default_test_mappings": [
           {
             "test_code": "VIH-1",
@@ -99,7 +100,7 @@
         },
         "catalog": {
           "revision": 1,
-          "revisionFingerprint": "sha256:8d099084227b7de083a6f8f0511234c8f09540534182a380060fe921a7f28c21",
+          "revisionFingerprint": "sha256:a39955225875ee8cc4ae2a5a0c587acd5c9e376749485ef48ef1eca2cefcf770",
           "recognitionFingerprint": "sha256:5c0de42e1135b772b23e4c1ea04b0162b30fe36fc08ecef76a70108ba031be26",
           "source": "SHIPPED",
           "status": "ACTIVE",
@@ -111,6 +112,49 @@
         "action": "SHIPPED",
         "actor": "distribution",
         "markedAt": "2026-08-19T00:00:00Z"
+      },
+      "controlRecognitionSummary": {
+        "recognitionFingerprint": "sha256:5c0de42e1135b772b23e4c1ea04b0162b30fe36fc08ecef76a70108ba031be26",
+        "mode": "RULES",
+        "description": "Any listed condition identifies a control result.",
+        "affirmedNoControlResults": false,
+        "conditions": [
+          {
+            "key": "positive-control-task",
+            "kind": "FIELD_VALUE_EQUALS",
+            "sourceLabel": "Control task",
+            "value": "Positive",
+            "description": "Control task equals Positive"
+          },
+          {
+            "key": "negative-control-task",
+            "kind": "FIELD_VALUE_EQUALS",
+            "sourceLabel": "Control task",
+            "value": "Negative",
+            "description": "Control task equals Negative"
+          },
+          {
+            "key": "standard-control-task",
+            "kind": "FIELD_VALUE_EQUALS",
+            "sourceLabel": "Control task",
+            "value": "Standard",
+            "description": "Control task equals Standard"
+          },
+          {
+            "key": "positive-control-prefix",
+            "kind": "SPECIMEN_ID_STARTS_WITH",
+            "sourceLabel": "Specimen ID",
+            "value": "C+",
+            "description": "Specimen ID starts with C+"
+          },
+          {
+            "key": "negative-control-prefix",
+            "kind": "SPECIMEN_ID_STARTS_WITH",
+            "sourceLabel": "Specimen ID",
+            "value": "C-",
+            "description": "Specimen ID starts with C-"
+          }
+        ]
       }
     }
   ]

contracts/analyzer/v1/profile-catalog-entry.schema.json

@@ -4,7 +4,7 @@
   "title": "OpenELIS Analyzer Bridge profile catalog entry v1",
   "type": "object",
   "additionalProperties": false,
-  "required": ["profile", "publication"],
+  "required": ["profile", "publication", "controlRecognitionSummary"],
   "properties": {
     "profile": {
       "$ref": "https://openelis-global.org/contracts/analyzer/v1/analyzer-profile.schema.json"
@@ -27,6 +27,83 @@
         "actor": { "type": "string", "minLength": 1 },
         "markedAt": { "type": "string", "format": "date-time" }
       }
+    },
+    "controlRecognitionSummary": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["recognitionFingerprint", "mode", "description", "affirmedNoControlResults", "conditions"],
+      "properties": {
+        "recognitionFingerprint": {
+          "type": "string",
+          "pattern": "^sha256:[0-9a-f]{64}$"
+        },
+        "mode": { "enum": ["RULES", "NONE"] },
+        "description": { "type": "string", "minLength": 1 },
+        "affirmedNoControlResults": { "type": "boolean" },
+        "conditions": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "additionalProperties": false,
+            "required": ["key", "kind", "sourceLabel", "value", "description"],
+            "properties": {
+              "key": { "type": "string", "minLength": 1 },
+              "kind": {
+                "enum": [
+                  "SPECIMEN_ID_STARTS_WITH",
+                  "CONFIGURED_SPECIMEN_ID_PATTERN",
+                  "FIELD_VALUE_EQUALS",
+                  "FIELD_VALUE_CONTAINS"
+                ]
+              },
+              "sourceLabel": { "type": "string", "minLength": 1 },
+              "value": { "type": ["string", "null"] },
+              "description": { "type": "string", "minLength": 1 },
+              "controlLevel": { "type": ["string", "null"] },
+              "controlType": { "type": ["string", "null"] }
+            },
+            "allOf": [
+              {
+                "if": {
+                  "properties": {
+                    "kind": { "const": "CONFIGURED_SPECIMEN_ID_PATTERN" }
+                  }
+                },
+                "then": {
+                  "properties": {
+                    "value": { "type": "null" }
+                  }
+                },
+                "else": {
+                  "properties": {
+                    "value": { "type": "string", "minLength": 1 }
+                  }
+                }
+              }
+            ]
+          }
+        }
+      },
+      "allOf": [
+        {
+          "if": { "properties": { "mode": { "const": "RULES" } } },
+          "then": {
+            "properties": {
+              "affirmedNoControlResults": { "const": false },
+              "conditions": { "minItems": 1 }
+            }
+          }
+        },
+        {
+          "if": { "properties": { "mode": { "const": "NONE" } } },
+          "then": {
+            "properties": {
+              "affirmedNoControlResults": { "const": true },
+              "conditions": { "maxItems": 0 }
+            }
+          }
+        }
+      ]
     }
   }
 }

src/main/java/org/itech/ahb/config/AnalyzerRegistryConfig.java

@@ -4,6 +4,10 @@
 import lombok.Data;
 import lombok.Setter;
 import lombok.extern.slf4j.Slf4j;
+import org.itech.ahb.fhir.TabularFileLayout;
+import org.itech.ahb.profile.AstmResultRecordSelection;
+import org.itech.ahb.profile.ControlResultRecognition;
+import org.itech.ahb.profile.TabularResultValueSelection;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.context.annotation.Configuration;
 
@@ -264,6 +268,12 @@ public void setIdentifierPattern(String identifierPattern) {
         /** Number of metadata rows to skip before header detection (default 0). */
         private int skipRows;
 
+        /** Profile-owned instructions for locating the tabular result header. */
+        private TabularFileLayout tabularFileLayout;
+
+        /** Profile-owned precedence for selecting a reportable tabular value. */
+        private TabularResultValueSelection tabularResultValueSelection;
+
         /**
          * Profile-derived file-wide analyzer test code for FILE exports that do
          * not carry a row-level {@code testCode}. This is materialized only when
@@ -281,14 +291,11 @@ public void setIdentifierPattern(String identifierPattern) {
         /** OE test codes this analyzer is allowed to emit (whitelist, not a default). */
         private Set<String> mappedTestCodes = Collections.emptySet();
 
-        /** Control-result recognition rules from the pinned Bridge profile. */
-        private java.util.List<org.itech.ahb.qc.QcRule> qcRules = new java.util.ArrayList<>();
+        /** Complete control-result recognition from the pinned Bridge profile. */
+        private ControlResultRecognition controlResultRecognition;
 
-        /**
-         * Transitional parser input. The registration contract never populates
-         * operational control lots; target recognition comes only from the profile.
-         */
-        private java.util.List<org.itech.ahb.qc.ControlLotDto> controlLots = new java.util.ArrayList<>();
+        /** Profile-owned selection of ASTM R records that carry reportable results. */
+        private AstmResultRecordSelection astmResultRecordSelection;
 
         /**
          * Analyzer test_code → LOINC mapping materialized from the pinned profile's

src/main/java/org/itech/ahb/controller/ASTMServerRunnerTrigger.java

@@ -5,12 +5,14 @@
 import java.util.List;
 import lombok.extern.slf4j.Slf4j;
 import org.itech.ahb.lib.astm.servlet.ASTMServlet;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
 import org.springframework.stereotype.Component;
 
 /**
  * Component for triggering an ASTM server runner for each ASTM transmission servlet.
  */
 @Component
+@ConditionalOnProperty(name = "org.itech.ahb.astm.enabled", havingValue = "true", matchIfMissing = true)
 @Slf4j
 public class ASTMServerRunnerTrigger {
 

src/main/java/org/itech/ahb/controller/FileUploadController.java

@@ -373,7 +373,12 @@ public ResponseEntity<Map<String, Object>> scanFile(
             Files.write(tempFile, file.getBytes(),
                     StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING);
 
-            ScanResult scanResult = scanner.scan(tempFile, columnMappings, allowedCodes, getSynonyms(entry));
+            ScanResult scanResult = scanner.scan(
+                    tempFile,
+                    columnMappings,
+                    entry.getTabularResultValueSelection(),
+                    allowedCodes,
+                    getSynonyms(entry));
             if (scanResult instanceof ScanResult.SelfDeclared selfDeclared) {
                 response.put("suggestion", selfDeclared.testCode());
                 response.put("confidence", "selfDeclared");