Merge pull request #161 from SynBioDex/InteractionNodes

Interaction nodes
SynBioDex · May 3, 2021 · b00240b · b00240b
2 parents aab7a74 + 9c2d3ab
commit b00240b
Show file tree

Hide file tree

Showing 23 changed files with 1,497 additions and 295 deletions.
diff --git a/SBOLCanvasBackend/src/data/InteractionInfo.java b/SBOLCanvasBackend/src/data/InteractionInfo.java
@@ -1,32 +1,25 @@
 package data;
 
-import utils.Converter;
+import java.util.Hashtable;
 
 public class InteractionInfo extends Info {
 
 	private String displayID;
 	private String interactionType;
 	private String fromParticipationType;
 	private String toParticipationType;
-	private String fromURI;
-	private String toURI;
-
-	public String getFromURI() {
-		return fromURI;
-	}
-
-	public void setFromURI(String fromURI) {
-		this.fromURI = fromURI;
-	}
-
-	public String getToURI() {
-		return toURI;
-	}
+	private Hashtable<String, String> sourceRefinement;
+	private Hashtable<String, String> targetRefinement;
+	private Hashtable<String, String> fromURI;
+	private Hashtable<String, String> toURI;
 
-	public void setToURI(String toURI) {
-		this.toURI = toURI;
+	public InteractionInfo() {
+		sourceRefinement = new Hashtable<String, String>();
+		targetRefinement = new Hashtable<String, String>();
+		fromURI = new Hashtable<String, String>();
+		toURI = new Hashtable<String, String>();
 	}
-
+	
 	public String getDisplayID() {
 		return displayID;
 	}
@@ -59,7 +52,39 @@ public void setToParticipationType(String toParticipationType) {
 		this.toParticipationType = toParticipationType;
 	}
 
+	public Hashtable<String, String> getSourceRefinement() {
+		return sourceRefinement;
+	}
+
+	public void setSourceRefinement(Hashtable<String, String> sourceRefinement) {
+		this.sourceRefinement = sourceRefinement;
+	}
+
+	public Hashtable<String, String> getTargetRefinement() {
+		return targetRefinement;
+	}
+
+	public void setTargetRefinement(Hashtable<String, String> targetRefinement) {
+		this.targetRefinement = targetRefinement;
+	}
+
+	public Hashtable<String, String> getFromURI() {
+		return fromURI;
+	}
+
+	public void setFromURI(Hashtable<String, String> fromURI) {
+		this.fromURI = fromURI;
+	}
+
+	public Hashtable<String, String> getToURI() {
+		return toURI;
+	}
+
+	public void setToURI(Hashtable<String, String> toURI) {
+		this.toURI = toURI;
+	}
+
 	public String getFullURI() {
-		return Converter.URI_PREFIX+'/'+this.displayID;
+		return this.uriPrefix + '/' + this.displayID;
 	}
 }
diff --git a/SBOLCanvasBackend/src/servlets/Data.java b/SBOLCanvasBackend/src/servlets/Data.java
@@ -39,6 +39,15 @@ protected void doGet(HttpServletRequest request, HttpServletResponse response) t
 				body = gson.toJson(SBOLData.getRefinement(parent));
 			} else if (request.getPathInfo().equals("/interactions")) {
 				body = gson.toJson(SBOLData.getInteractions());
+			}else if (request.getPathInfo().equals("/interactionRoles")) {
+				body = gson.toJson(SBOLData.getInteractionRoles());
+			}else if (request.getPathInfo().equals("/interactionRoleRefine")) {
+				String parent = request.getParameter("parent");
+				if(parent == null) {
+					response.setStatus(HttpStatus.SC_BAD_REQUEST);
+					return;
+				}
+				body = gson.toJson(SBOLData.getInteractionRoleRefinement(parent));
 			}
 
 			// write it to the response body

diff --git a/SBOLCanvasBackend/src/utils/Converter.java b/SBOLCanvasBackend/src/utils/Converter.java
@@ -14,6 +14,7 @@
 
 import data.CombinatorialInfo;
 import data.Info;
+import data.InteractionInfo;
 
 public class Converter {
 
@@ -24,6 +25,7 @@ public class Converter {
 	// data constants
 	public static final int INFO_DICT_INDEX = 0;
 	public static final int COMBINATORIAL_DICT_INDEX = 1;
+	public static final int INTERACTION_DICT_INDEX = 2;
 
 	// style constants
 	protected static final String STYLE_CIRCUIT_CONTAINER = "circuitContainer";
@@ -37,6 +39,7 @@ public class Converter {
 	protected static final String STYLE_INTERACTION = "interactionGlyph";
 	protected static final String STYLE_MODULE_VIEW = "moduleViewCell";
 	protected static final String STYLE_COMPONENT_VIEW = "componentViewCell";
+	protected static final String STYLE_INTERACTION_NODE = "interactionNodeGlyph";
 
 	static {
 		// Necessary for encoding/decoding GlyphInfo and InteractionInfo
@@ -45,6 +48,7 @@ public class Converter {
 
 	protected Hashtable<String, Info> infoDict;
 	protected Hashtable<String, CombinatorialInfo> combinatorialDict;
+	protected Hashtable<String, InteractionInfo> interactionDict;
 	protected LayoutHelper layoutHelper;
 
 	/**
@@ -107,6 +111,13 @@ public boolean filter(Object arg0) {
 		}
 	};
 
+	static Filter interactionNodeFilter = new Filter() {
+		@Override
+		public boolean filter(Object arg0) {
+			return arg0 instanceof mxCell && ((mxCell) arg0).getStyle().contains(STYLE_INTERACTION_NODE);
+		}
+	};
+
 	protected static URI getParticipantType(boolean source, Set<URI> interactionTypes) {
 		if (interactionTypes.contains(SystemsBiologyOntology.BIOCHEMICAL_REACTION)) {
 			return source ? SystemsBiologyOntology.REACTANT : SystemsBiologyOntology.PRODUCT;