Merge pull request #187 from SynBioDex/encoding-fixes-and-logout-on-u…

…pload Encoding fixes and logout on upload
SynBioDex · Sep 9, 2021 · 71c4ae6 · 71c4ae6
2 parents f367e63 + a78f928
commit 71c4ae6
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Showing 5 changed files with 43 additions and 30 deletions.
diff --git a/SBOLCanvasBackend/src/utils/Converter.java b/SBOLCanvasBackend/src/utils/Converter.java
@@ -6,8 +6,6 @@
 
 import javax.xml.namespace.QName;
 
-import org.sbolstandard.core2.SystemsBiologyOntology;
-
 import com.mxgraph.io.mxCodecRegistry;
 import com.mxgraph.model.mxCell;
 import com.mxgraph.model.mxGraphModel.Filter;
@@ -119,22 +117,21 @@ public boolean filter(Object arg0) {
 	};
 
 	protected static URI getParticipantType(boolean source, Set<URI> interactionTypes) {
-		if (interactionTypes.contains(SystemsBiologyOntology.BIOCHEMICAL_REACTION)) {
-			return source ? SystemsBiologyOntology.REACTANT : SystemsBiologyOntology.PRODUCT;
-		} else if (interactionTypes.contains(SystemsBiologyOntology.CONTROL)) {
-			return source ? SystemsBiologyOntology.MODIFIER : SystemsBiologyOntology.MODIFIED;
-		} else if (interactionTypes.contains(SystemsBiologyOntology.DEGRADATION)) {
-			return SystemsBiologyOntology.REACTANT;
-		} else if (interactionTypes.contains(SystemsBiologyOntology.GENETIC_PRODUCTION)) {
-			return source ? SystemsBiologyOntology.TEMPLATE : SystemsBiologyOntology.PRODUCT;
-		} else if (interactionTypes.contains(SystemsBiologyOntology.INHIBITION)) {
-			return source ? SystemsBiologyOntology.INHIBITOR : SystemsBiologyOntology.INHIBITED;
-		} else if (interactionTypes.contains(SystemsBiologyOntology.NON_COVALENT_BINDING)) {
-			return source ? SystemsBiologyOntology.REACTANT : SystemsBiologyOntology.PRODUCT;
-		} else if (interactionTypes.contains(SystemsBiologyOntology.STIMULATION)) {
-			return source ? SystemsBiologyOntology.STIMULATOR : SystemsBiologyOntology.STIMULATED;
+		URI interactionType = null;
+		for(URI interactionURI : SBOLData.interactions.values()) {
+			if(interactionTypes.contains(interactionURI)) {
+				interactionType = interactionURI;
+				break;
+			}
+		}
+		if(interactionType == null) {
+			return null;
+		}
+		if(source) {
+			return SBOLData.interactionSourceRoles.get(interactionType);
+		}else {
+			return SBOLData.interactionTargetRoles.get(interactionType);
 		}
-		return null;
 	}
 
 	static QName createQName(String name) {

diff --git a/SBOLCanvasBackend/src/utils/MxToSBOL.java b/SBOLCanvasBackend/src/utils/MxToSBOL.java
@@ -255,16 +255,6 @@ private void createModuleDefinition(SBOLDocument document, mxGraph graph, mxGrap
 				.toArray(mxCell[]::new);
 
 		ModuleInfo modInfo = (ModuleInfo) infoDict.get(viewCell.getId());
-		if (modInfo.getUriPrefix() == null)
-			modInfo.setUriPrefix(URI_PREFIX);
-		ModuleDefinition modDef = document.createModuleDefinition(modInfo.getUriPrefix(), modInfo.getDisplayID(),
-				modInfo.getVersion());
-		layoutHelper.createGraphicalLayout(modDef.getIdentity(), modDef.getDisplayId() + "_Layout");
-
-		// text boxes
-		if (textBoxes.length > 0) {
-			attachTextBoxAnnotation(model, viewCell, modDef.getIdentity());
-		}
 
 		// if the uri is one of the synbiohub ones, just add the layout
 		boolean layoutOnly = false;
@@ -281,6 +271,23 @@ private void createModuleDefinition(SBOLDocument document, mxGraph graph, mxGrap
 			}
 		}
 
+		if (modInfo.getUriPrefix() == null || modInfo.getUriPrefix().equals(""))
+			modInfo.setUriPrefix(URI_PREFIX);
+
+		ModuleDefinition modDef = null;
+		if(layoutOnly) {
+			modDef = document.getModuleDefinition(new URI(modInfo.getFullURI()));
+		}else {
+			modDef = document.createModuleDefinition(modInfo.getUriPrefix(), modInfo.getDisplayID(),
+					modInfo.getVersion());			
+		}
+		layoutHelper.createGraphicalLayout(modDef.getIdentity(), modDef.getDisplayId() + "_Layout");
+
+		// text boxes
+		if (textBoxes.length > 0) {
+			attachTextBoxAnnotation(model, viewCell, modDef.getIdentity());
+		}
+
 		// proteins
 		for (mxCell protein : proteins) {
 			// proteins also have glyphInfos
@@ -513,7 +520,8 @@ private void linkModuleDefinition(SBOLDocument document, mxGraph graph, mxGraphM
 				Set<Interaction> interactions = modDef.getInteractions();
 				// find the interaction with the correct identity
 				for (Interaction inter : interactions) {
-					if (inter.getIdentity().toString().equals((String) intInfo.getFullURI())) {
+					// TODO don't use startsWith here, inter.getIdentity() is including the version number, which isn't tracked in the front end
+					if (inter.getIdentity().toString().startsWith((String) intInfo.getFullURI())) {
 						interaction = inter;
 						break;
 					}

diff --git a/SBOLCanvasBackend/src/utils/SBOLData.java b/SBOLCanvasBackend/src/utils/SBOLData.java
@@ -126,7 +126,7 @@ public class SBOLData {
 		interactionSourceRoles.put(SystemsBiologyOntology.BIOCHEMICAL_REACTION, SystemsBiologyOntology.REACTANT);
 		interactionSourceRoles.put(SystemsBiologyOntology.NON_COVALENT_BINDING, SystemsBiologyOntology.REACTANT);
 		interactionSourceRoles.put(SystemsBiologyOntology.DEGRADATION, SystemsBiologyOntology.REACTANT);
-		interactionSourceRoles.put(SystemsBiologyOntology.GENETIC_PRODUCTION, SystemsBiologyOntology.REACTANT);
+		interactionSourceRoles.put(SystemsBiologyOntology.GENETIC_PRODUCTION, SystemsBiologyOntology.TEMPLATE);
 		interactionSourceRoles.put(SystemsBiologyOntology.CONTROL, SystemsBiologyOntology.MODIFIER);
 		interactionSourceRoles.put(SystemsBiologyOntology.DISSOCIATION, SystemsBiologyOntology.REACTANT);
 

diff --git a/SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.html b/SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.html
@@ -57,7 +57,8 @@ <h1 mat-dialog-title *ngIf="importMode">Import</h1>
   </div>
 
   <div mat-dialog-actions>
-    <button mat-button [disabled]="loginDisabled()" (click)="onLoginClick()">Login</button>
+    <button mat-button *ngIf="!loginDisabled()" [disabled]="!registry" (click)="onLoginClick()">Login</button>
+    <button mat-button *ngIf="loginDisabled()" [disabled]="!registry" (click)="onLogoutClick()">Logout</button>
     <button mat-button (click)="onCancelClick()">Cancel</button>
     <button *ngIf="!importMode" mat-button [disabled]="!finishCheck()" (click)="onUploadClick()">Upload</button>
     <button *ngIf="importMode" mat-button [disabled]="!finishCheck()" (click)="onImportClick()">Import</button>

diff --git a/SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.ts b/SBOLCanvasFrontend/src/app/upload-graph/upload-graph.component.ts
@@ -102,6 +102,13 @@ export class UploadGraphComponent implements OnInit {
     });
   }
 
+  async onLogoutClick() {
+    this.working = true;
+    await this.loginService.logout(this.registry);
+    this.working = false;
+    this.updateCollections();
+  }
+
   onCreateCollectionClick() {
     this.dialog.open(CollectionCreationComponent, {data: {registry: this.registry}}).afterClosed().subscribe(result => {
       if(result)