@memoarchitect/ontology 0.6.4 → 0.6.5

package/examples/gpca-pump/model/catalog/gpca_behavior_modes.sysml

@@ -13,13 +13,19 @@ package memo_examples_gpca_pump_model_catalog_gpca_behavior_modes {
     // auto-initiate on the prescribed schedule (REQ 24), with no
     // external trigger. Mode-tree containment edges (Composes)
     // live in gpca_trace.sysml.
+    // Audit scope: this is a requirements-level therapy-mode abstraction, not
+    // a full transcription of CITE-009's monolithic Stateflow chart. The
+    // source chart also contains detailed Configuration, Alarms,
+    // System_Monitor, Log, and Infusion_Manager state behavior that remains
+    // outside this compact mode view.
     // ═════════════════════════════════════════════════════════════
     state topLevelModeMachine : StateMachine {
         attribute :>> id = "BM-001";
         attribute :>> name = "TopLevelModeMachine";
         attribute :>> machineKind = "hierarchical state machine";
         attribute :>> executionSemantics = "single-step synchronous; sub-modes inherit all parent-mode requirements";
-        attribute :>> sourceReference = "CITE-001: CriSys GPCA System Requirements (2013), §4.1 Fig 4.1";
+        attribute fidelityScope = "Requirements-derived therapy mode hierarchy; partial abstraction of CITE-009, not a state-for-state Stateflow transcription";
+        attribute :>> sourceReference = "CITE-001: CriSys GPCA System Requirements (2013), §4.1 Fig 4.1; CITE-009: CriSys PCA Pump Software Model";
     }
 
     // ── Mode states (Fig 4.1) ───────────────────────────────────

package/examples/gpca-pump/model/catalog/gpca_interfaces.sysml

@@ -2,6 +2,7 @@ package memo_examples_gpca_pump_model_catalog_gpca_interfaces {
     private import ScalarValues::*;
 
     private import memo_architecture_logical_interfaces::*;
+    private import memo_architecture_realization_physical::*;
     private import memo_architecture_functional_functions::*;
     private import memo_examples_gpca_pump_model_catalog_gpca_architecture::*;
     private import memo_examples_gpca_pump_model_catalog_gpca_behavior_subsystems::*;
@@ -572,7 +573,10 @@ package memo_examples_gpca_pump_model_catalog_gpca_interfaces {
         attribute :>> sourceReference = "CITE-001: CriSys GPCA System Requirements (2013), §3.5 Hospital Pharmacy Database Interface";
     }
 
-    // ── Device-boundary exchanges (GPCA_Device.aadl level) ─────
+    // ── MEMO functional-to-physical allocation abstractions ────
+    // These four exchanges summarize requirements-derived physical design
+    // intent. They are not the named port connections in GPCA_Device.aadl;
+    // the exact AADL feature topology is authored below and in gpca_trace.
     part exSensorVector : ComponentExchange {
         attribute :>> id = "CE-001";
         attribute :>> name = "SensorStatusVectorExchange";
@@ -584,7 +588,7 @@ package memo_examples_gpca_pump_model_catalog_gpca_interfaces {
         ref :>> allocatedExchanges = lfSensorAcquisition;
         attribute :>> direction = DirectionKind::input;
         attribute :>> timingSemantics = "immediate (same-step delivery, Communication_Properties::Timing => immediate)";
-        attribute :>> sourceReference = "CITE-002: CriSys GPCA AADL v2.0, packages/GPCA_Device.aadl";
+        attribute :>> sourceReference = "MEMO design extension allocated from LF-001; not a GPCA_Device.aadl connection";
     }
     part exFlowCommand : ComponentExchange {
         attribute :>> id = "CE-002";
@@ -597,7 +601,7 @@ package memo_examples_gpca_pump_model_catalog_gpca_interfaces {
         ref :>> allocatedExchanges = lfFlowCommand;
         attribute :>> direction = DirectionKind::output;
         attribute :>> timingSemantics = "immediate (same-step delivery, Communication_Properties::Timing => immediate)";
-        attribute :>> sourceReference = "CITE-002: CriSys GPCA AADL v2.0, packages/GPCA_Device.aadl";
+        attribute :>> sourceReference = "MEMO design extension allocated from LF-002; not a GPCA_Device.aadl connection";
     }
     part exAlarmAnnunciation : ComponentExchange {
         attribute :>> id = "CE-003";
@@ -610,7 +614,7 @@ package memo_examples_gpca_pump_model_catalog_gpca_interfaces {
         ref :>> allocatedExchanges = lfAlarmSignal;
         attribute :>> direction = DirectionKind::output;
         attribute :>> timingSemantics = "immediate (same-step delivery, Communication_Properties::Timing => immediate)";
-        attribute :>> sourceReference = "CITE-002: CriSys GPCA AADL v2.0, packages/GPCA_Device.aadl";
+        attribute :>> sourceReference = "MEMO design extension allocated from LF-003; not a GPCA_Device.aadl connection";
     }
     part exPrescriptionEntry : ComponentExchange {
         attribute :>> id = "CE-004";
@@ -623,9 +627,34 @@ package memo_examples_gpca_pump_model_catalog_gpca_interfaces {
         ref :>> allocatedExchanges = lfPrescriptionEntry;
         attribute :>> direction = DirectionKind::input;
         attribute :>> timingSemantics = "immediate (same-step delivery, Communication_Properties::Timing => immediate)";
-        attribute :>> sourceReference = "CITE-002: CriSys GPCA AADL v2.0, packages/GPCA_Device.aadl";
+        attribute :>> sourceReference = "MEMO design extension allocated from LF-004; not a GPCA_Device.aadl connection";
     }
 
+    // ── GPCA_Device and hardware-subsystem ports (AADL, 1:1) ───
+    // The published AADL hardware packages are interface wrappers: they do
+    // not decompose into the individual physical parts modelled elsewhere in
+    // this MEMO example. These features and their connections are therefore
+    // kept exact and separate from that extended physical design content.
+    part devOpCmdIn : PhysicalPort { attribute :>> id = "PORT-DEV-01"; attribute :>> name = "OP_CMD_IN"; attribute :>> direction = DirectionKind::input; attribute :>> sourceReference = "CITE-002: GPCA_Device.aadl"; }
+    part devDbIn : PhysicalPort { attribute :>> id = "PORT-DEV-02"; attribute :>> name = "DB_IN"; attribute :>> direction = DirectionKind::input; attribute :>> sourceReference = "CITE-002: GPCA_Device.aadl"; }
+    part devPresIn : PhysicalPort { attribute :>> id = "PORT-DEV-03"; attribute :>> name = "PRES_IN"; attribute :>> direction = DirectionKind::input; attribute :>> sourceReference = "CITE-002: GPCA_Device.aadl"; }
+    part devPatientIn : PhysicalPort { attribute :>> id = "PORT-DEV-04"; attribute :>> name = "PATIENT_IN"; attribute :>> direction = DirectionKind::input; attribute :>> sourceReference = "CITE-002: GPCA_Device.aadl"; }
+    part devGpcaOut : PhysicalPort { attribute :>> id = "PORT-DEV-05"; attribute :>> name = "GPCA_OUT"; attribute :>> direction = DirectionKind::output; attribute :>> sourceReference = "CITE-002: GPCA_Device.aadl"; }
+
+    part snsOpCmdIn : PhysicalPort { attribute :>> id = "PORT-SNS-01"; attribute :>> name = "OP_CMD_IN"; attribute :>> direction = DirectionKind::input; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+    part snsDbIn : PhysicalPort { attribute :>> id = "PORT-SNS-02"; attribute :>> name = "DB_IN"; attribute :>> direction = DirectionKind::input; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+    part snsPresIn : PhysicalPort { attribute :>> id = "PORT-SNS-03"; attribute :>> name = "PRES_IN"; attribute :>> direction = DirectionKind::input; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+    part snsPatientIn : PhysicalPort { attribute :>> id = "PORT-SNS-04"; attribute :>> name = "PATIENT_IN"; attribute :>> direction = DirectionKind::input; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+    part snsOpCmdOut : PhysicalPort { attribute :>> id = "PORT-SNS-05"; attribute :>> name = "OP_CMD_OUT"; attribute :>> direction = DirectionKind::output; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+    part snsPresOut : PhysicalPort { attribute :>> id = "PORT-SNS-06"; attribute :>> name = "PRES_OUT"; attribute :>> direction = DirectionKind::output; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+    part snsPatientOut : PhysicalPort { attribute :>> id = "PORT-SNS-07"; attribute :>> name = "PATIENT_OUT"; attribute :>> direction = DirectionKind::output; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+    part snsSensorOut : PhysicalPort { attribute :>> id = "PORT-SNS-08"; attribute :>> name = "SENSOR_OUT"; attribute :>> direction = DirectionKind::output; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+    part snsConstOut : PhysicalPort { attribute :>> id = "PORT-SNS-09"; attribute :>> name = "CONST_OUT"; attribute :>> direction = DirectionKind::output; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+    part snsDbOut : PhysicalPort { attribute :>> id = "PORT-SNS-10"; attribute :>> name = "DB_OUT"; attribute :>> direction = DirectionKind::output; attribute :>> sourceReference = "CITE-002: GPCA_HW_Sensors.aadl"; }
+
+    part actGpcaSwIn : PhysicalPort { attribute :>> id = "PORT-ACT-01"; attribute :>> name = "GPCA_SW_IN"; attribute :>> direction = DirectionKind::input; attribute :>> sourceReference = "CITE-002: GPCA_HW_Actuators.aadl"; }
+    part actGpcaOut : PhysicalPort { attribute :>> id = "PORT-ACT-02"; attribute :>> name = "GPCA_OUT"; attribute :>> direction = DirectionKind::output; attribute :>> sourceReference = "CITE-002: GPCA_HW_Actuators.aadl"; }
+
     // ── GPCA_SW top-level ports (AADL GPCA_SW.aadl features) ────
     part portOpCmdIn : SoftwarePort {
         attribute :>> id = "PORT-01"; attribute :>> name = "OP_CMD_IN";

package/examples/gpca-pump/model/catalog/gpca_risk.sysml

@@ -71,6 +71,15 @@ package memo_examples_gpca_pump_model_catalog_gpca_risk {
         attribute :>> year = "2009";
     }
 
+    part citeCriSysSoftwareBehavior : Citation {
+        attribute :>> id = "CITE-009";
+        attribute :>> name = "CriSysGpcaSoftwareBehaviorModel";
+        attribute :>> source = "PCA Pump Software Model (Simulink/Stateflow) — University of Minnesota CriSys";
+        attribute :>> section = "Infusion Pump Software Model Stateflow chart";
+        attribute :>> uri = "https://crisys.cs.umn.edu/downloads/gpca/PCA_Pump_SoftwareModel.mdl";
+        attribute :>> year = "undated";
+    }
+
     // ── Shared risk matrix ───────────────────────────────────────────
     part riskMatrix : RiskMatrix {
         attribute :>> id = "RMX-001";

package/examples/gpca-pump/model/catalog/gpca_trace.sysml

@@ -435,14 +435,38 @@ package memo_examples_gpca_pump_model_catalog_gpca_trace {
     connection : Composes connect parent ::> gpcaSoftware to child ::> portDbIn;
     connection : Composes connect parent ::> gpcaSoftware to child ::> portGpcaSwOut;
 
-    // ── Device-boundary interconnect (GPCA_Device.aadl; CE-001..004,
-    //    CITE-002) — hardware ↔ software-port connection topology ──
-    connection : ExchangesWith connect source ::> gpcaDeviceSensors to target ::> portSensorIn;
-    connection : ExchangesWith connect source ::> portGpcaSwOut to target ::> pumpMotorAssembly;
-    connection : ExchangesWith connect source ::> portGpcaSwOut to target ::> audibleAlarm;
-    connection : ExchangesWith connect source ::> portGpcaSwOut to target ::> operatorDisplay;
-    connection : ExchangesWith connect source ::> operatorKeypad to target ::> portPresIn;
-    connection : ExchangesWith connect source ::> operatorKeypad to target ::> portOpCmdIn;
+    // ── Device/subsystem feature ownership (published AADL, 1:1) ──
+    connection : Composes connect parent ::> gpcaDevice to child ::> devOpCmdIn;
+    connection : Composes connect parent ::> gpcaDevice to child ::> devDbIn;
+    connection : Composes connect parent ::> gpcaDevice to child ::> devPresIn;
+    connection : Composes connect parent ::> gpcaDevice to child ::> devPatientIn;
+    connection : Composes connect parent ::> gpcaDevice to child ::> devGpcaOut;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsOpCmdIn;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsDbIn;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsPresIn;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsPatientIn;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsOpCmdOut;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsPresOut;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsPatientOut;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsSensorOut;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsConstOut;
+    connection : Composes connect parent ::> gpcaDeviceSensors to child ::> snsDbOut;
+    connection : Composes connect parent ::> gpcaActuators to child ::> actGpcaSwIn;
+    connection : Composes connect parent ::> gpcaActuators to child ::> actGpcaOut;
+
+    // ── GPCA_Device.Impl connections (GPCA_Device.aadl, 1:1) ──
+    connection : ExchangesWith connect source ::> devOpCmdIn to target ::> snsOpCmdIn;
+    connection : ExchangesWith connect source ::> devDbIn to target ::> snsDbIn;
+    connection : ExchangesWith connect source ::> devPresIn to target ::> snsPresIn;
+    connection : ExchangesWith connect source ::> devPatientIn to target ::> snsPatientIn;
+    connection : ExchangesWith connect source ::> snsOpCmdOut to target ::> portOpCmdIn;
+    connection : ExchangesWith connect source ::> snsPresOut to target ::> portPresIn;
+    connection : ExchangesWith connect source ::> snsPatientOut to target ::> portPatientIn;
+    connection : ExchangesWith connect source ::> snsSensorOut to target ::> portSensorIn;
+    connection : ExchangesWith connect source ::> snsConstOut to target ::> portConstIn;
+    connection : ExchangesWith connect source ::> snsDbOut to target ::> portDbIn;
+    connection : ExchangesWith connect source ::> portGpcaSwOut to target ::> actGpcaSwIn;
+    connection : ExchangesWith connect source ::> actGpcaOut to target ::> devGpcaOut;
 
     // ── Risk chains (ISO 14971, GIIP causal-tree structure) ─────
     // Categorized causes converge on each hazard (GIIP Tables 2-9

package/examples/gpca-pump/model/views/logical_device_interconnect_view.sysml

@@ -19,8 +19,8 @@ package memo_examples_gpca_pump_model_views_logical_device_interconnect_view {
         attribute :>> id = "VIEW-LOG-003";
         attribute :>> name = "GPCA_DeviceInterconnectView";
         attribute :>> title = "GPCA Device Interconnect View";
-        attribute :>> shortDescription = "Device-level interconnection: hardware assemblies wired to the software system's boundary ports.";
-        attribute :>> longDescription = "Interconnection-kind view of the GPCA device per GPCA_Device.aadl: sensor and actuator assemblies, the GPCA software system with its seven AADL boundary ports (OP_CMD_IN, PRES_IN, PATIENT_IN, SENSOR_IN, CONST_IN, DB_IN, GPCA_SW_OUT) pinned on its boundary, the eight software subcomponents nested inside, and the ExchangesWith connection topology (device-boundary CE-001..004 plus the GPCA_SW.Impl internal connections). Rendered through the KK-3 Interconnection view template.";
+        attribute :>> shortDescription = "AADL device-level interconnection: GPCA_HW_Sensors, GPCA_SW, and GPCA_HW_Actuators with their declared boundary features.";
+        attribute :>> longDescription = "Source-faithful interconnection view of GPCA_Device.Impl: exactly the three AADL subcomponents (GPCA_HW_Sensors, GPCA_SW, GPCA_HW_Actuators), the device and subsystem boundary ports, and the twelve declared port connections. MEMO physical-design additions such as the controller board, power sources, enclosure, and individual sensors/actuators are intentionally excluded because the published AADL v2.0 model does not declare them as GPCA_Device.Impl subcomponents. Drill into GPCA_SW to inspect its eight subcomponents and 42 internal connections; use the connection-density control to switch between bundled summary and full fidelity.";
         attribute :>> outputKind = (ViewOutputKind::diagram);
         attribute :>> presentationKind = (PresentationKind::internalDiagram);
         attribute :>> viewKind = DiagramViewKind::interconnection;
@@ -32,7 +32,7 @@ package memo_examples_gpca_pump_model_views_logical_device_interconnect_view {
         part :>> selectionQuery {
             attribute :>> id = "QRY-LOG-003";
             attribute :>> name = "GPCA_DeviceInterconnectQuery";
-            attribute :>> includeElementKinds = ("HardwareAssembly", "SoftwareSystem", "SoftwareModule", "SoftwarePort");
+            attribute :>> includeElementIds = ("gpcaDevice", "gpcaDeviceSensors", "gpcaSoftware", "gpcaActuators", "devOpCmdIn", "devDbIn", "devPresIn", "devPatientIn", "devGpcaOut", "snsOpCmdIn", "snsDbIn", "snsPresIn", "snsPatientIn", "snsOpCmdOut", "snsPresOut", "snsPatientOut", "snsSensorOut", "snsConstOut", "snsDbOut", "portOpCmdIn", "portPresIn", "portPatientIn", "portSensorIn", "portConstIn", "portDbIn", "portGpcaSwOut", "actGpcaSwIn", "actGpcaOut", "tlm", "systemStatus", "alarm", "config", "infusionMgr", "systemMonitor", "logging", "outputBus");
             attribute :>> includeRelationshipKinds = ("ExchangesWith", "Composes");
             attribute :>> includeLayers = ("logical_structure", "software_structure", "interfaces");
             attribute :>> selectionExpression = "product == 'GPCA'";

package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@memoarchitect/ontology",
-  "version": "0.6.4",
+  "version": "0.6.5",
   "packageManager": "pnpm@9.15.0",
-  "description": "MEMO \u2014 Medical Engineering Modelling Ontology. Pure SysML v2 medical-device ontology with native constraints, portable to any conformant SysML v2 tool (SysIDE, SysON, sysand).",
+  "description": "MEMO — Medical Engineering Modelling Ontology. Pure SysML v2 medical-device ontology with native constraints, portable to any conformant SysML v2 tool (SysIDE, SysON, sysand).",
   "scripts": {
     "build": "bash scripts/build-kpar.sh",
     "check": "bash scripts/build-kpar.sh",

package/src/rules/ontology/ontology_invariants.sysml

@@ -19,6 +19,19 @@ package memo_rules_ontology {
         attribute predicateExpression = "acyclic(composes)";
         constraint { true }
     }
+    constraint def nestedPartConnectedRule {
+        attribute id = "AR-IBD-001";
+        attribute appliesTo = "MemoPart";
+        attribute severity = RuleSeverityKind::warning;
+        attribute rationaleText = "A structural part nested inside another part should expose at least one modeled interface connector. Passive or intentionally isolated parts may retain this warning with an explicit modelling rationale.";
+        attribute predicateExpression = "hasConnectorInComposition";
+        // Graph-aware structural rule, evaluated by Memo Architect's rule
+        // engine: it lifts port endpoints to their owning part, ignores
+        // composition/trace/deployment links, and includes a connected child's
+        // containing assemblies. The generic KerML expression evaluator cannot
+        // represent that transitive containment query.
+        constraint { true }
+    }
     constraint def connectorEndpointsExistRule {
         attribute id = "CR-ONT-002";
         attribute appliesTo = "ComponentExchange";

package/src/viewpoints/definitions/memo_viewpoint_definitions.sysml

@@ -34,6 +34,7 @@ package memo_viewpoints_definitions {
 
     part def ViewSelectionQuery specializes MemoPart {
         attribute includeElementKinds : String[*];
+        attribute includeElementIds : String[*];
         attribute includeRelationshipKinds : String[*];
         attribute includeLayers : String[*];
         attribute includeConcerns : ConcernKind[*];
@@ -79,6 +80,7 @@ package memo_viewpoints_definitions {
 
     part def ViewInclusionRule specializes MemoPart {
         attribute includeElementKinds : String[*];
+        attribute includeElementIds : String[*];
         attribute includeRelationshipKinds : String[*];
         attribute includeLayers : String[*];
         attribute includeConcerns : ConcernKind[*];