sys-bio · longxf21 · Nov 20, 2022 · Dec 1, 2022 · Dec 2, 2022 · Dec 2, 2022
diff --git a/vscode-antimony/all-requirements.txt b/vscode-antimony/all-requirements.txt
@@ -19,3 +19,5 @@ bioservices==1.8.3
 # ols_client==0.0.9
 AMAS-sb==0.0.1
 orjson==3.8.0
+SBMLDiagrams
+tellurium
diff --git a/vscode-antimony/package.json b/vscode-antimony/package.json
@@ -29,6 +29,7 @@
 		"onCommand:antimony.switchIndicationOff",
 		"onCommand:antimony.convertAntimonyToSBML",
 		"onCommand:antimony.convertSBMLToAntimony",
+		"onCommand:antimony.convertAntimonyToDiagram",
 		"onCommand:antimony.startSBMLWebview",
 		"onCommand:antimony.startAntimonyWebview",
 		"onCustomEditor:antimony.sbmlEditor",
@@ -122,6 +123,10 @@
 				"command": "antimony.convertSBMLToAntimony",
 				"title": "Convert to Antimony"
 			},
+			{
+				"command": "antimony.convertAntimonyToDiagram",
+				"title": "Convert to Diagram"
+			},
 			{
 				"command": "antimony.startSBMLWebview",
 				"title": "preview SBML",
@@ -189,6 +194,12 @@
 					"title": "Convert to Antimony",
 					"group": "1_modification",
 					"when": "editorLangId == xml"
+				},
+				{
+					"command": "antimony.convertAntimonyToDiagram",
+					"title": "Convert to Diagram",
+					"group": "1_modification",
+					"when": "editorLangId == antimony"
 				}
 			],
 			"editor/title": [

diff --git a/vscode-antimony/src/extension.ts b/vscode-antimony/src/extension.ts
@@ -130,6 +130,13 @@ export async function activate(context: vscode.ExtensionContext) {
 		vscode.commands.registerCommand('antimony.convertSBMLToAntimony',
 			(...args: any[]) => convertSBMLToAntimony(context, args)));
 
+	// SBMLDiagram
+	context.subscriptions.push(
+		vscode.commands.registerCommand('antimony.convertAntimonyToDiagram',
+			(...args: any[]) => {
+				convertAntimonyToDiagram(context, args);
+			}));
+
 	// custom editor
 	context.subscriptions.push(await SBMLEditorProvider.register(context, client));
 	context.subscriptions.push(await AntimonyEditorProvider.register(context, client));
@@ -281,6 +288,84 @@ async function checkConversionResult(result, type) {
 	}
 }
 
+async function convertAntimonyToDiagram(context: vscode.ExtensionContext, args: any[]) {
+	if (!client) {
+		utils.pythonInterpreterError();
+		return;
+	}
+	await client.onReady();
+
+	await vscode.commands.executeCommand("workbench.action.focusActiveEditorGroup");
+
+	const doc = vscode.window.activeTextEditor.document;
+	const uri = doc.uri.toString();
+
+	let speciesStr;
+	vscode.commands.executeCommand('antimony.getDiagramQuickpick', uri).then(async (result) => {
+		speciesStr = result;
+		let speciesList = speciesStr.species_list.split(' ');
+		let selectedSpeciesList = await vscode.window.showQuickPick(speciesList, {canPickMany: true, placeHolder: 'select species to include in your diagram'});
+		if (selectedSpeciesList && selectedSpeciesList.length === 0) {
+			vscode.window.showErrorMessage('Please select at least one species!');
+		} else {
+			const options: vscode.OpenDialogOptions = {
+				openLabel: "Select",
+				canSelectFolders: true,
+				canSelectFiles: false,
+				canSelectMany: false,
+				filters: {
+					'Images': ['png']
+				},
+				title: "Select a location to save your SBML diagram"
+			};
+			vscode.window.showOpenDialog(options).then(fileUri => {
+				if (fileUri && fileUri[0]) {
+				 let diagram;
+						vscode.commands.executeCommand('antimony.antFiletoDiagram', vscode.window.activeTextEditor.document, 
+							fileUri[0].fsPath, selectedSpeciesList).then(async (result) => {
+						 let error = await checkSBMLDiagramResult(result);
+						 diagram = result;
+						 if (!diagram.error) {
+							 const panel = vscode.window.createWebviewPanel(
+								 'antimony',
+								 'SBMLDiagram',
+								 vscode.ViewColumn.Two,
+								 {
+								   localResourceRoots: [vscode.Uri.file(path.dirname(diagram.file))]
+								 }
+							 );
+							 const pngSrc = panel.webview.asWebviewUri(vscode.Uri.file(diagram.file));
+							 panel.webview.html = getWebviewContent(pngSrc);
+						 }
+					 });
+				}
+			});
+		}
+	});
+}
+
+function getWebviewContent(uri: vscode.Uri) {
+	return `<!DOCTYPE html>
+  <html lang="en">
+  <head>
+	  <meta charset="UTF-8">
+	  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+	  <title>SBMLDiagram</title>
+  </head>
+  <body>
+	  <img src=${uri} width="300" />
+  </body>
+  </html>`;
+  }
+
+async function checkSBMLDiagramResult(result) {
+	if (result.error) {
+		vscode.window.showErrorMessage(`Could not convert file to diagram: ${result.error}`);
+	} else {
+		vscode.window.showInformationMessage(`${result.msg}`);
+	}
+}
+
 async function createAnnotationDialog(context: vscode.ExtensionContext, args: any[]) {
 	// wait till client is ready, or the Python server might not have started yet.
 	// note: this is necessary for any command that might use the Python language server.
@@ -290,7 +375,6 @@ async function createAnnotationDialog(context: vscode.ExtensionContext, args: an
 	}
 	await client.onReady();
 	await vscode.commands.executeCommand("workbench.action.focusActiveEditorGroup");
-
 	// dialog for annotation
 	const selection = vscode.window.activeTextEditor.selection;
 

diff --git a/vscode-antimony/src/server/main.py b/vscode-antimony/src/server/main.py
@@ -36,6 +36,8 @@
 import time
 from AMAS import recommender, species_annotation
 from bioservices import ChEBI
+import SBMLDiagrams
+import tellurium as te
 
 # TODO remove this for production
 logging.basicConfig(filename='vscode-antimony-dep.log', filemode='w', level=logging.DEBUG)
@@ -149,6 +151,47 @@ def sbml_file_to_ant_file(ls: LanguageServer, args):
             'file': full_path_name
         }
 
+@server.thread()
+@server.command('antimony.getDiagramQuickpick')
+def ant_file_to_sbml_file(ls: LanguageServer, args):
+    uri = args[0]
+    doc = server.workspace.get_document(uri)
+    antfile_cache = get_antfile(doc)
+    reaction_list = antfile_cache.analyzer.reaction_list
+    species_set = set()
+    for species_names, reaction_part_str in reaction_list:
+        species_set.update(species_names)
+    species_list = list(species_set)
+    species_list.sort()
+    return {
+        'species_list': " ".join(species_list)
+    }
+
+@server.thread()
+@server.command('antimony.antFiletoDiagram')
+def ant_file_to_sbml_file(ls: LanguageServer, args):
+    ant = args[0].fileName
+    output_dir = args[1]
+    selected_species_list = args[2]
+    model_str = 'model *temp()\n'
+    reaction_list = antfile_cache.analyzer.reaction_list
+    for react_prod_list, reaction_str in reaction_list:
+        if any((match := item) in react_prod_list for item in selected_species_list):
+            model_str += reaction_str + '\n'
+    model_str += 'end'
+    r = te.loada(model_str)
+    sbmlStr = r.getSBML()
+    df = SBMLDiagrams.load(sbmlStr)
+    model_name = os.path.basename(ant)
+    full_path_name = os.path.join(output_dir, os.path.splitext(model_name)[0]+'_diagram.png')
+    df.autolayout()
+    df.draw(output_fileName=full_path_name,showReactionIds=True)
+    return {
+        'msg': 'Diagram has been exported to {}'.format(output_dir),
+        'file': full_path_name
+    }
+
+
 @server.thread()
 @server.command('antimony.sendType')
 def get_type(ls: LanguageServer, args) -> dict[str, str]:
@@ -167,7 +210,6 @@ def get_type(ls: LanguageServer, args) -> dict[str, str]:
     symbols= antfile_cache.symbols_at(position)[0]
 
     symbol = symbols[0].type.__str__()
-    vscode_logger.info("symbol: " + symbol)
     return {
         'symbol': symbol
     }

diff --git a/vscode-antimony/src/server/stibium/stibium/analysis.py b/vscode-antimony/src/server/stibium/stibium/analysis.py
@@ -92,6 +92,7 @@ def __init__(self, root: FileNode, path: str):
         self.unnamed_events_num = 0
         base_scope = BaseScope()
         self.reaction_item = set()
+        self.reaction_list = list()
         for child in root.children:
             if isinstance(child, ErrorToken):
                 continue
@@ -492,13 +493,19 @@ def handle_reaction(self, scope: AbstractScope, reaction: Reaction, insert: bool
             else:
                 self.table.insert(QName(scope, name), SymbolType.Reaction, reaction, comp=comp)
 
+        species_names = set()
         for species in chain(reaction.get_reactants(), reaction.get_products()):
             if insert:
                 self.import_table.insert(QName(scope, species.get_name()), SymbolType.Species, comp=comp)
                 self.import_table.get(QName(scope, species.get_name()))[0].in_reaction = True
             else:
                 self.table.insert(QName(scope, species.get_name()), SymbolType.Species, comp=comp)
                 self.table.get(QName(scope, species.get_name()))[0].in_reaction = True
+            species_names.add(species.get_name_text())
+        reaction_str = reaction.to_string()
+        reaction_part_str = reaction_str.split(';')[0] + ';'
+        self.reaction_list.append((species_names, reaction_part_str))
+
         rate_law = reaction.get_rate_law()
         if rate_law is not None:
             self.handle_arith_expr(scope, rate_law, insert)

diff --git a/vscode-antimony/src/server/stibium/stibium/ant_types.py b/vscode-antimony/src/server/stibium/stibium/ant_types.py
@@ -417,6 +417,17 @@ def get_comp(self):
         if self.children[6] is not None:
             return self.children[6]
         return None
+
+    def to_string(self) -> str:
+        ret = ''
+        if isinstance(self, LeafNode):
+            ret += self.text
+        else:
+            for node in self.descendants():
+                if isinstance(node, LeafNode):
+                    ret += node.text
+        return ret
+
 
 @dataclass
 class InteractionName(TrunkNode):