Merge pull request #171 from sys-bio/sbmlwarning

Sbmlwarning

examples/BioModels/1.ant

@@ -89,6 +89,7 @@ model *BIOMD0000000001()
   const comp1, t2, kr_0, kr_1, kf_2, kr_2, kr_3, kr_4, kf_5, kr_5, kf_6, kr_6;
   const kr_7, kr_8, kf_9, kr_9, kf_10, kr_10, kf_11, kr_11, kr_12, kr_13;
   const kf_14, kr_14, kf_15, kr_15, kf_16, kr_16;
+  unit kf_17 = 1.66057788110262e;
 
   // Display Names:
   comp1 is "compartment1";

vscode-antimony/src/extension.ts

@@ -216,8 +216,31 @@ export async function activate(context: vscode.ExtensionContext) {
   if (path.extname(vscode.window.activeTextEditor.document.fileName) === '.xml' && roundTripping) {
     triggerSBMLEditor(vscode.window.activeTextEditor.document, sbmlFileNameToPath);
   }
+  if (fileExtension == '.xml') {
+    vscode.commands.executeCommand('antimony.checkSbml', doc.uri.path).then((result: any) => {
+      if (result === true) {
+        vscode.window.showWarningMessage("This SBML file contains notes, model history, algebraic rules and unsupported packages. Proceed conversion to Antimony with caution.")
+      }
+    });
+  }
 }
 
+vscode.window.onDidChangeActiveTextEditor(() => {
+  const activeTextEditor = vscode.window.activeTextEditor;
+  if (activeTextEditor) {
+    const doc = activeTextEditor.document;
+    const uri = doc.uri.toString();
+    const fileExtension = path.extname(uri);
+    if (fileExtension == '.xml') {
+      vscode.commands.executeCommand('antimony.checkSbml', doc.uri.path).then((result: any) => {
+        if (result === true) {
+          vscode.window.showWarningMessage("This SBML file contains notes, model history, algebraic rules, and/or unsupported packages. Proceed conversion to Antimony with caution.");
+        }
+      });
+    }
+  }
+});
+
 async function triggerSBMLEditor(event: TextDocument, sbmlFileNameToPath: Map<any, any>) {
   await client.onReady();
 
@@ -696,7 +719,6 @@ export async function createVirtualEnv(context: vscode.ExtensionContext) {
       .then(async selection => {
         if (selection === 'Yes') {
           installEnv();
-          vscode.env.openExternal(vscode.Uri.parse("https://github.com/sys-bio/vscode-antimony#installation-required-1"));
         } else if (selection === 'No') {
           vscode.window.showInformationMessage('The default python interpreter will be used.');
         }
@@ -893,7 +915,6 @@ async function deleteVirtualEnv(message) {
           promptToReloadWindow("Reload for changes to take effect.")
         }
       } else if (selection === 'No') {
-        vscode.env.openExternal(vscode.Uri.parse("https://github.com/sys-bio/vscode-antimony#installation-required-1"));
         vscode.window.showWarningMessage(`The extension will not work without deleting and reinstalling the virtual environment.`, {modal: true}, action)
         .then(selectedAction => {
           if (selectedAction === action) {

vscode-antimony/src/server/main.py

@@ -10,6 +10,8 @@
 
 import antimony
 
+from libsbml import *
+
 sys.path.append(os.path.join(EXTENSION_ROOT, "server", "stibium"))
 
 from stibium.parse import AntimonyParser
@@ -51,7 +53,6 @@
 antfile_cache = None
 uri = None
 
-
 #### Annotations ####
 @server.command('antimony.getAnnotated')
 def get_annotated(ls: LanguageServer, args):
@@ -239,6 +240,68 @@ def get_rate_law_dict(ls: LanguageServer, args):
         }
     return reader.relevant_rate_laws
 
+#### Check sbml files ####
+@server.thread()
+@server.command('antimony.checkSbml')
+def check_sbml(ls: LanguageServer, args):
+  feature_exists = False
+  sbml = args[0]
+  sbml_doc = readSBML(sbml)
+  model = sbml_doc.getModel()
+
+  # Check for packages
+  if model.isPackageEnabled('comp'):
+    # vscode_logger.info('Comp Package is enabled')
+    feature_exists = True
+  elif model.isPackageEnabled('fbc'):
+    # vscode_logger.info('FBC Package is enabled')
+    feature_exists = True
+  elif model.isPackageEnabled('distrib'):
+    # vscode_logger.info('Distrib Package is enabled')
+    feature_exists = True
+  elif model.isPackageEnabled('layout'):
+    # vscode_logger.info('Layout Package is enabled')
+    feature_exists = True
+  elif model.isPackageEnabled('render'):
+    # vscode_logger.info('Render Package is enabled')
+    feature_exists = True
+  elif model.isPackageEnabled('spatial'):
+    # vscode_logger.info('Spatial Package is enabled')
+    feature_exists = True
+  elif model.isPackageEnabled('multi'):
+    # vscode_logger.info('Multi Package is enabled')
+    feature_exists = True
+  elif model.isPackageEnabled('qual'):
+    # vscode_logger.info('Qual Package is enabled')
+    feature_exists = True
+
+  # Check for model history
+  if model.isSetModelHistory():
+    # vscode_logger.info('Model History is set')
+    feature_exists = True
+
+  # Check for Notes
+  elementsList = sbml_doc.getListOfAllElements()
+  # vscode_logger.info('List of Elements: ')
+  # vscode_logger.info(sbml_doc.getListOfAllElements())
+  # vscode_logger.info('elementsList')
+  for x in elementsList:
+      # vscode_logger.info(x)
+      if (x.isSetNotes()):
+        # vscode_logger.info('Notes are set')
+        feature_exists = True
+
+  # Check for Algebraic Rules
+  for r in range(model.getNumRules()):
+    rule = model.getRule(r)
+    # vscode_logger.info('Rule Type Code: ')
+    # vscode_logger.info(rule.getTypeCode())
+    if rule.getTypeCode() == SBML_ALGEBRAIC_RULE:
+      # vscode_logger.info('Algebraic Rule is set')
+      feature_exists = True
+
+  return feature_exists
+
 # @server.thread()
 # @server.command('antimony.recommender')
 # def recommend(ls: LanguageServer, args):