Move export validation from backend errors to frontend warnings

SBOLCanvasBackend/src/utils/MxToSBOL.java

@@ -168,15 +168,23 @@ public SBOLDocument setupDocument(InputStream graphStream) throws IOException, U
 				.toArray(mxCell[]::new);
 
 				for(mxCell glyph: glyphs){
-					createComponentDefinition(document, graph, model, glyph);
+					try {
+						createComponentDefinition(document, graph, model, glyph);
+					} catch (Exception e) {
+						System.err.println("Warning: SBOL export skipped glyph: " + e.getMessage());
+					}
 				}
 
 				if (layoutHelper.getGraphicalLayout(URI.create((String) circuitContainer.getValue())) != null){
 					continue;
 				}
 
 				// Create Component Definition for the container itself
-				createComponentDefinition(document, graph, model, circuitContainer);
+				try {
+					createComponentDefinition(document, graph, model, circuitContainer);
+				} catch (Exception e) {
+					System.err.println("Warning: SBOL export skipped container: " + e.getMessage());
+				}
 			}
 		}
 
@@ -190,12 +198,15 @@ public SBOLDocument setupDocument(InputStream graphStream) throws IOException, U
 			mxCell[] molecularSpecies = Arrays.stream(mxGraphModel.filterCells(viewChildren, molecularSpeciesFilter))
 			.toArray(mxCell[]::new);
 
-			if (viewCell.getStyle().equals(STYLE_MODULE_VIEW) || circuitContainers.length > 1 || molecularSpecies.length > 0) {
-				// module definitions
-				createModuleDefinition(document, graph, model, viewCell);
-			} else {
-				// component definitions
-				attachTextBoxAnnotation(model, viewCell, URI.create(viewCell.getId()));
+			try {
+				if (STYLE_MODULE_VIEW.equals(viewCell.getStyle()) || circuitContainers.length > 1 || molecularSpecies.length > 0) {
+					createModuleDefinition(document, graph, model, viewCell);
+				} else {
+					// component definitions
+					attachTextBoxAnnotation(model, viewCell, URI.create(viewCell.getId()));
+				}
+			} catch (Exception e) {
+				System.err.println("Warning: SBOL export skipped view cell: " + e.getMessage());
 			}
 		}
 
@@ -209,7 +220,11 @@ public SBOLDocument setupDocument(InputStream graphStream) throws IOException, U
 			for (mxCell cell : cells) {
 				if (handledContainers.contains((String) cell.getValue()))
 					continue;
-				linkComponentDefinition(document, graph, model, cell);
+				try {
+					linkComponentDefinition(document, graph, model, cell);
+				} catch (Exception e) {
+					System.err.println("Warning: SBOL export skipped link: " + e.getMessage());
+				}
 				handledContainers.add((String) cell.getValue());
 			}
 		}
@@ -221,24 +236,39 @@ public SBOLDocument setupDocument(InputStream graphStream) throws IOException, U
 					.toArray(mxCell[]::new);
 			mxCell[] molecularSpecies = Arrays.stream(mxGraphModel.filterCells(viewChildren, molecularSpeciesFilter))
 					.toArray(mxCell[]::new);
-			if (viewCell.getStyle().equals(STYLE_MODULE_VIEW) || circuitContainers.length > 1 || molecularSpecies.length > 0) {
-				// module definitions
-				linkModuleDefinition(document, graph, model, viewCell);
+			if (STYLE_MODULE_VIEW.equals(viewCell.getStyle()) || circuitContainers.length > 1 || molecularSpecies.length > 0) {
+				try {
+					linkModuleDefinition(document, graph, model, viewCell);
+				} catch (Exception e) {
+					System.err.println("Warning: SBOL export skipped link: " + e.getMessage());
+				}
 			}
 		}
 
 		// create the combinatorials
 		for (CombinatorialInfo info : combinatorialDict.values()) {
-			createCombinatorial(document, graph, model, info);
+			try {
+				createCombinatorial(document, graph, model, info);
+			} catch (Exception e) {
+				System.err.println("Warning: SBOL export skipped combinatorial: " + e.getMessage());
+			}
 		}
 
 		// link the combinatorials
 		for (CombinatorialInfo info : combinatorialDict.values()) {
-			linkCombinatorial(document, graph, model, info);
+			try {
+				linkCombinatorial(document, graph, model, info);
+			} catch (Exception e) {
+				System.err.println("Warning: SBOL export skipped combinatorial link: " + e.getMessage());
+			}
 		}
 
 		// write events as GenericTopLevel objects
-		writeEvents(document, graph);
+		try {
+			writeEvents(document, graph);
+		} catch (Exception e) {
+			System.err.println("Warning: SBOL export skipped events: " + e.getMessage());
+		}
 
 		return document;
 	}
@@ -370,7 +400,7 @@ private void createComponentDefinition(SBOLDocument document, mxGraph graph, mxG
 		// store extra mxGraph information
 		URI identity = URI.create(glyphInfo.getFullURI());
 		layoutHelper.createGraphicalLayout(identity, glyphInfo.getDisplayID() + "_Layout");
-		if(circuitContainer.getStyle().equals(STYLE_CIRCUIT_CONTAINER)){
+		if(STYLE_CIRCUIT_CONTAINER.equals(circuitContainer.getStyle())){
 
 			Object[] containerChildren = mxGraphModel.getChildCells(model, circuitContainer, true, false);
 			mxCell backboneCell = (mxCell) mxGraphModel.filterCells(containerChildren, backboneFilter)[0];

SBOLCanvasFrontend/src/app/graph-helpers.ts

@@ -2073,7 +2073,7 @@ export class GraphHelpers extends GraphBase {
         this.graph.getModel().execute(new GraphEdits.infoEdit(cell0, eventInfo, null, GraphBase.EVENT_DICT_INDEX))
     }
 
-    protected getFromEventDict(eventURI: string): EventInfo {
+    public getFromEventDict(eventURI: string): EventInfo {
         const cell0 = this.graph.getModel().getCell(0)
         if (!cell0.value[GraphBase.EVENT_DICT_INDEX]) {
             return null
@@ -2142,7 +2142,7 @@ export class GraphHelpers extends GraphBase {
         this.graph.getModel().execute(new GraphEdits.infoEdit(cell0, info, null, GraphBase.INTERACTION_DICT_INDEX))
     }
 
-    protected getFromInteractionDict(interactionURI: string): InteractionInfo {
+    public getFromInteractionDict(interactionURI: string): InteractionInfo {
         const cell0 = this.graph.getModel().getCell(0)
         return cell0.value[GraphBase.INTERACTION_DICT_INDEX][interactionURI]
     }

SBOLCanvasFrontend/src/app/graph.service.ts

@@ -70,18 +70,14 @@ export class GraphService extends GraphHelpers {
                     },
                     error: err => {
                         console.error('[GraphService] SBOL export failed:', err)
-                        const message = typeof err.error === 'string' ? err.error : err.message || 'SBOL export failed'
-                        embeddedService.postMessage({
-                            error: { type: 'sbol-export', message: message }
-                        })
                     }
                 })
             }
         })
 
-        // SBML auto-export pipeline (2000ms debounce)
+        // SBML auto-export pipeline (1000ms debounce)
         modelChange$
-        .pipe(debounceTime(2000))
+        .pipe(debounceTime(1000))
         .subscribe(graphXml => {
             if (embeddedService.isAppEmbedded()) {
                 console.debug('[GraphService] Model changed. Sending SBML to parent.')
@@ -91,10 +87,6 @@ export class GraphService extends GraphHelpers {
                     },
                     error: err => {
                         console.error('[GraphService] SBML export failed:', err)
-                        const message = typeof err.error === 'string' ? err.error : err.message || 'SBML export failed'
-                        embeddedService.postMessage({
-                            error: { type: 'sbml-export', message: message }
-                        })
                     }
                 })
             }

SBOLCanvasFrontend/src/app/home/home.component.ts

@@ -29,7 +29,7 @@ export class HomeComponent implements OnInit, ComponentCanDeactivate {
   leftBarOpened = true;
 
   constructor(private graphService: GraphService, private titleService: Title, private embeddedService: EmbeddedService) {
-    this.titleService.setTitle('SBOL Canvas');
+    this.titleService.setTitle('SBOLCanvas');
   }
 
   ngOnInit() {

SBOLCanvasFrontend/src/app/landing-page/landing-page.component.html

@@ -23,10 +23,10 @@
       Biologists often face the challenge of effectively communicating DNA sequences and their behaviors. An increasingly popular solution is SBOL, the Synthetic Biology Open Language. It is a diagram syntax that models genetic systems, allowing for both abstract visualizations and detailed data. Unfortunately, the complexity of creating SBOL documents is limiting this powerful language’s growth. SBOL, while characterized by graphic models, is lacking tools for graphical editing. Until now.
       </p>
       <p class="about-text">
-      SBOL Canvas is an open source web-based graphical editor that opens synthetic biology design to anyone from students to advanced researchers. Users will enjoy a simple interface for creating diagrams that are both artistic and scientific. By interfacing with existing SBOL databases, SBOL Canvas lets users share their designs and easily reference the research of others. This editor significantly lowers SBOL’s barrier to entry, helping it carry synthetic biology to new heights.
+      SBOLCanvas is an open source web-based graphical editor that opens synthetic biology design to anyone from students to advanced researchers. Users will enjoy a simple interface for creating diagrams that are both artistic and scientific. By interfacing with existing SBOL databases, SBOLCanvas lets users share their designs and easily reference the research of others. This editor significantly lowers SBOL’s barrier to entry, helping it carry synthetic biology to new heights.
       </p>
       <p class="about-text">
-        SBOL Canvas is supported in part by the <a href="https://sbolstandard.org/sbol-industrial/" target="_blank">SBOL Industrial Consortium</a>. 
+        SBOLCanvas is supported in part by the <a href="https://sbolstandard.org/sbol-industrial/" target="_blank">SBOL Industrial Consortium</a>. 
         It is currently being developed by those in the Genetic Logic Lab led by Dr. Chris Myers and is part of the Synthetic Biology Data Exchange Group. 
       </p>
     </div>

SBOLCanvasFrontend/src/app/landing-page/landing-page.component.ts

@@ -14,7 +14,7 @@ export class LandingPageComponent implements OnInit {
   version = "Development";
 
   constructor(private titleService: Title) {
-    this.titleService.setTitle("SBOL Canvas About");
+    this.titleService.setTitle("SBOLCanvas About");
     this.hash = versions.revision;
     this.version = versions.version;
   }

SBOLCanvasFrontend/src/app/problems/problems.component.ts

@@ -1,4 +1,4 @@
-import { Component } from '@angular/core'
+import { Component, OnDestroy, OnInit } from '@angular/core'
 import { GraphService } from '../graph.service'
 
 
@@ -8,18 +8,23 @@ import { GraphService } from '../graph.service'
     styleUrls: ['./problems.component.css']
 })
 
-export class ProblemsComponent {
+export class ProblemsComponent implements OnInit, OnDestroy {
 
     warnings: string[]
     errors: string[]
+    private intervalId: number
 
     constructor(private graphService: GraphService) { }
 
     ngOnInit() {
         this.warnings = []
         this.errors = []
 
-        setInterval(this.validate.bind(this), 750)
+        this.intervalId = window.setInterval(this.validate.bind(this), 750)
+    }
+
+    ngOnDestroy() {
+        clearInterval(this.intervalId)
     }
 
     validate() {
@@ -29,6 +34,8 @@ export class ProblemsComponent {
         // Validation functions
         this.validateCurrentView(warnings, errors)
         this.validateComponents(warnings, errors)
+        this.validateBackbones(warnings)
+        this.validateInteractionsAndEvents(warnings)
         // more here...
 
         // Transpose to separate errors and warnings
@@ -37,7 +44,6 @@ export class ProblemsComponent {
     }
 
     validateCurrentView(warnings: string[], errors: string[]) {
-
         const currentView = this.graphService.getCurrentRoot()
         const children = currentView.children || []
 
@@ -63,6 +69,7 @@ export class ProblemsComponent {
 
     validateComponent(component, warnings: string[], errors: string[]) {
         const info = this.graphService.lookupInfo(component.value)
+        if (!info) return
         const sequence = (info.sequence || '').toUpperCase()
         const version = (info.version || '')
 
@@ -92,4 +99,106 @@ export class ProblemsComponent {
         version && !compliant &&
             warnings.push(`Component '${info.displayID}' has incompliant version: ${version}`)
     }
+
+    validateBackbones(warnings: string[]) {
+        const currentView = this.graphService.getCurrentRoot()
+        const containers = (currentView.children || []).filter(c => c.isCircuitContainer())
+
+        for (const container of containers) {
+            const children = container.children || []
+            const glyphs = children.filter(c => c.isSequenceFeatureGlyph && c.isSequenceFeatureGlyph())
+
+            if (glyphs.length > 0 && !glyphs.some(g => {
+                const info = this.graphService.lookupInfo(g.value)
+                return info && info.partRole && info.partRole.includes('Promoter')
+            })) {
+                const containerInfo = this.graphService.lookupInfo(container.value)
+                const name = (containerInfo && containerInfo.displayID) || 'unnamed'
+                warnings.push(`Backbone '${name}': no promoter (skipped in SBML)`)
+            }
+        }
+    }
+
+    validateInteractionsAndEvents(warnings: string[]) {
+        const currentView = this.graphService.getCurrentRoot()
+        const directChildren = currentView.children || []
+        const nestedChildren = directChildren.map(c => c.children || []).flat()
+        const allCells = [...directChildren, ...nestedChildren]
+
+        // Disconnected interaction edges
+        const interactions = allCells.filter(c => c.isInteraction && c.isInteraction())
+        const regulationByTarget: { [key: string]: { inhibition: boolean, stimulation: boolean } } = {}
+
+        for (const edge of interactions) {
+            const info = this.graphService.getFromInteractionDict(edge.value)
+            if (!info) continue
+
+            const type = info.interactionType
+            const isDegradation = type === 'Degradation'
+
+            // Degradation edges naturally have no target (species degrades into nothing)
+            if (!edge.source || (!edge.target && !isDegradation)) {
+                const connectedEnd = edge.source || edge.target
+                const endInfo = connectedEnd ? this.graphService.lookupInfo(connectedEnd.value) : null
+                const endName = (endInfo && (endInfo.name || endInfo.displayID)) || 'unknown'
+                const missing = !edge.source ? 'no source' : 'no target'
+                warnings.push(`${type} edge on '${endName}': ${missing}`)
+                continue
+            }
+            if (type === 'Inhibition' || type === 'Stimulation') {
+                const targetId = edge.target.value || 'unknown'
+                if (!regulationByTarget[targetId])
+                    regulationByTarget[targetId] = { inhibition: false, stimulation: false }
+                if (type === 'Inhibition') regulationByTarget[targetId].inhibition = true
+                if (type === 'Stimulation') regulationByTarget[targetId].stimulation = true
+            }
+        }
+
+        for (const [targetId, reg] of Object.entries(regulationByTarget)) {
+            if (reg.inhibition && reg.stimulation) {
+                const info = this.graphService.lookupInfo(targetId)
+                const name = (info && info.name) || (info && info.displayID) || 'unknown'
+                warnings.push(`Promoter '${name}': mixed regulation (skipped in SBML)`)
+            }
+        }
+
+        // Complex formation nodes
+        const interactionNodes = allCells.filter(c => c.isInteractionNode && c.isInteractionNode())
+        for (const node of interactionNodes) {
+            const info = this.graphService.getFromInteractionDict(node.value)
+            if (!info) continue
+            const type = info.interactionType
+            if (type !== 'Biochemical Reaction' && type !== 'Non-Covalent Binding') continue
+
+            const edges = this.graphService.graph.getModel().getEdges(node) || []
+            const incoming = edges.filter(e => e.target === node)
+            const outgoing = edges.filter(e => e.source === node)
+
+            const reactantNames = incoming
+                .filter(e => e.source)
+                .map(e => {
+                    const ri = this.graphService.lookupInfo(e.source.value)
+                    return (ri && (ri.name || ri.displayID)) || '?'
+                })
+                .join(', ') || 'none'
+
+            if (outgoing.length === 0 || !outgoing[0].target)
+                warnings.push(`Complex formation (${reactantNames}): no product connection`)
+
+            for (const inEdge of incoming) {
+                if (!inEdge.source)
+                    warnings.push(`Complex formation (${reactantNames}): disconnected reactant edge`)
+            }
+        }
+
+        // Events without target species
+        const events = allCells.filter(c => c.isEvent && c.isEvent())
+        for (const event of events) {
+            const eventInfo = this.graphService.getFromEventDict(event.value)
+            if (!eventInfo) continue
+            const targetSpecies = (eventInfo.simulationData || {})['targetSpecies']
+            if (!targetSpecies)
+                warnings.push(`Event '${eventInfo.displayID || 'unnamed'}': no target species`)
+        }
+    }
 }

SBOLCanvasFrontend/src/app/toolbar/toolbar.component.html

@@ -64,10 +64,10 @@
             <!--    Help menu-->
             <button mat-stroked-button class="toolbar-row-button" [matMenuTriggerFor]="helpMenu">Help</button>
             <mat-menu #helpMenu="matMenu">
-                <button mat-menu-item class="toolbar-row-button" [matTooltip]="'Help using SBOL Canvas'"
+                <button mat-menu-item class="toolbar-row-button" [matTooltip]="'Help using SBOLCanvas'"
                     onClick="window.open('./tutorial')">Tutorial</button>
 
-                <button mat-menu-item class="toolbar-row-button" [matTooltip]="'About SBOL Canavs and its creators'"
+                <button mat-menu-item class="toolbar-row-button" [matTooltip]="'About SBOLCanvas and its creators'"
                     onClick="window.open('./about')">About</button>
 
                 <button mat-menu-item class="toolbar-row-button" [matTooltip]="'Links to Github issue tracker.'"