Merge f3b5d1d into e766ebe

src/plugins/simulation/SimulationExperimentView/src/simulationexperimentviewsimulationwidget.cpp

@@ -1014,10 +1014,10 @@ void SimulationExperimentViewSimulationWidget::initialize(bool pReloadingView)
                     information += QString(OutputTab+"<span"+OutputBad+"><strong>[%1:%2] %3</strong> %4.</span>"+OutputBrLn).arg(sedmlFileIssue.line())
                                                                                                                             .arg(sedmlFileIssue.column())
                                                                                                                             .arg(issueType)
-                                                                                                                            .arg(Core::formatMessage(sedmlFileIssue.message()));
+                                                                                                                            .arg(Core::formatMessage(sedmlFileIssue.message().toHtmlEscaped()));
                 } else {
                     information += QString(OutputTab+"<span"+OutputBad+"><strong>%1</strong> %2.</span>"+OutputBrLn).arg(issueType)
-                                                                                                                    .arg(Core::formatMessage(sedmlFileIssue.message()));
+                                                                                                                    .arg(Core::formatMessage(sedmlFileIssue.message().toHtmlEscaped()));
                 }
             }
         }
@@ -1937,7 +1937,6 @@ bool SimulationExperimentViewSimulationWidget::createSedmlFile(SEDMLSupport::Sed
         int graphPlotCounter;
         bool logAxisX;
         bool logAxisY;
-        char padding[2];   // Just for alignment
     } GraphsData;
 
     SimulationExperimentViewInformationGraphPanelAndGraphsWidget *graphPanelAndGraphsWidget = mContentsWidget->informationWidget()->graphPanelAndGraphsWidget();

src/plugins/support/SEDMLSupport/src/sedmlfile.cpp

@@ -145,6 +145,20 @@ libsedml::SedDocument * SedmlFile::sedmlDocument()
 
 //==============================================================================
 
+bool SedmlFile::isSedmlFile() const
+{
+    // Return whether our current SED-ML document is indeed a SED-ML file
+    // Note: a non-SED-ML file will result in our SED-ML document having one
+    //       error of id libsedml::SedNotSchemaConformant. So, we use this fact
+    //       to determine whether our current SED-ML document is indeed a SED-ML
+    //       file...
+
+    return    (mSedmlDocument->getNumErrors() != 1)
+           || (mSedmlDocument->getError(0)->getErrorId() != libsedml::SedNotSchemaConformant);
+}
+
+//==============================================================================
+
 bool SedmlFile::hasErrors() const
 {
     // Return whether our current SED-ML document has errors, be they normal
@@ -161,7 +175,7 @@ bool SedmlFile::load()
     // Check whether the file is already loaded and without any (fatal) errors
 
     if (!mLoadingNeeded)
-        return !hasErrors();
+        return isSedmlFile();
 
     mLoadingNeeded = false;
 
@@ -171,7 +185,7 @@ bool SedmlFile::load()
                          new libsedml::SedDocument(1, 3):
                          libsedml::readSedML(mFileName.toUtf8().constData());
 
-    return !hasErrors();
+    return isSedmlFile();
 }
 
 //==============================================================================
@@ -292,14 +306,20 @@ bool SedmlFile::isValid(const QString &pFileContents, SedmlFileIssues &pIssues)
             break;
         }
 
+        // Add the issue to our list, but only if it's not already in there
+        // Note: indeed, for some reasons, libSEDML may generate several copies
+        //       of the same error...
+
         static const QRegularExpression TrailingEmptyLinesRegEx = QRegularExpression("[\\n]*$");
 
         QString errorMessage = QString::fromStdString(error->getMessage()).remove(TrailingEmptyLinesRegEx);
+        SedmlFileIssue issue = SedmlFileIssue(issueType,
+                                              int(error->getLine()),
+                                              int(error->getColumn()),
+                                              errorMessage);
 
-        pIssues << SedmlFileIssue(issueType,
-                                  int(error->getLine()),
-                                  int(error->getColumn()),
-                                  errorMessage);
+        if (!pIssues.contains(issue))
+            pIssues << issue;
     }
 
     // Only consider our SED-ML document valid if it has no (fatal) errors
@@ -502,7 +522,8 @@ bool SedmlFile::isSupported()
         }
 
         // Make sure that the first simulation algorithm annotation, if any,
-        // contains at least the kind of information we would expect
+        // contains at least the kind of information we would expect, i.e.
+        // solver properties that somehow don't have KiSAO ids
 
         annotation = firstSimulationAlgorithm->getAnnotation();
 

src/plugins/support/SEDMLSupport/src/sedmlfile.h

@@ -147,6 +147,8 @@ class SEDMLSUPPORT_EXPORT SedmlFile : public StandardSupport::StandardFile
 
     void reset() override;
 
+    bool isSedmlFile() const;
+
     bool hasErrors() const;
 
     bool validListPropertyValue(const libsbml::XMLNode &pPropertyNode,

src/plugins/support/SEDMLSupport/src/sedmlfileissue.cpp

@@ -48,6 +48,18 @@ SedmlFileIssue::SedmlFileIssue(Type pType, const QString &pMessage) :
 
 //==============================================================================
 
+bool SedmlFileIssue::operator==(const SedmlFileIssue &pIssue) const
+{
+    // Return whether we are the same as the given issue
+
+    return     (mType == pIssue.mType)
+           &&  (mLine == pIssue.mLine)
+           &&  (mColumn == pIssue.mColumn)
+           && !mMessage.compare(pIssue.mMessage);
+}
+
+//==============================================================================
+
 SedmlFileIssue::Type SedmlFileIssue::type() const
 {
     // Return the issue's type

src/plugins/support/SEDMLSupport/src/sedmlfileissue.h

@@ -57,6 +57,8 @@ class SEDMLSUPPORT_EXPORT SedmlFileIssue
                             const QString &pMessage);
     explicit SedmlFileIssue(Type pType, const QString &pMessage);
 
+    bool operator==(const SedmlFileIssue &pIssue) const;
+
     Type type() const;
     int line() const;
     int column() const;

src/plugins/support/SimulationSupport/src/simulation.cpp

@@ -1148,7 +1148,7 @@ void Simulation::retrieveFileDetails(bool pRecreateRuntime)
 
         mRuntime = mCellmlFile?mCellmlFile->runtime(true):nullptr;
     } else {
-        if (mCellmlFile)
+        if (mCellmlFile && mRuntime)
             mRuntime->update(mCellmlFile, false);
     }
 }
@@ -1185,10 +1185,13 @@ void Simulation::save()
     // Make sure that our initial values are up to date and check for
     // modifications (which results in people being told that there are no
     // modifications, meaning that a view like the Simulation Experiment view
-    // will disable its reset buttons)
+    // will disable its reset buttons), but only if we have / still have a
+    // runtime
 
-    mData->updateInitialValues();
-    mData->checkForModifications();
+    if (mRuntime) {
+        mData->updateInitialValues();
+        mData->checkForModifications();
+    }
 }
 
 //==============================================================================