Exception handling and integration tests (#84)

* Working on improvement Exception handling [skip ci]
* Integration tests for data loading + CI attempt[skip ci]
* Integration tests in CIs [skip ci]
* Adding code coverage in the Ubuntu CI[skip ci]
* Graceful integration tests exit (threads issue) [skip ci]
* Disabling integration tests on Windows, hanging...[skip ci]
* Setting up CI for M1[skip ci]

.github/workflows/build_macos.yml

@@ -50,6 +50,13 @@ jobs:
         pip install matplotlib==3.3.4
         pip install --force-reinstall --no-cache-dir pyside6
 
+    - name: Integration tests
+      env:
+        DISPLAY: ':99.0'
+      run: |
+          pip install pytest-qt pytest-cov
+          pytest --cov=gui --cov=utils ${{github.workspace}}/integration_tests
+
     - name: Build software
       run: |
         pip install pyinstaller==5.13.2
@@ -72,8 +79,8 @@ jobs:
     - name: Make installer
       run: |
         git clone https://github.com/dbouget/quickpkg.git
-        quickpkg/quickpkg dist/Raidionics.app --output Raidionics-1.2.4-macOS.pkg
-        cp -r Raidionics-1.2.4-macOS.pkg dist/Raidionics-1.2.4-macOS-x86_64.pkg
+        quickpkg/quickpkg dist/Raidionics.app --output Raidionics-1.3.0-macOS.pkg
+        cp -r Raidionics-1.3.0-macOS.pkg dist/Raidionics-1.3.0-macOS-x86_64.pkg
 
     - name: Upload package
       uses: actions/upload-artifact@v4

.github/workflows/build_macos_arm.yml

@@ -49,6 +49,16 @@ jobs:
         mkdir ${{github.workspace}}/ANTs
         mv ${{github.workspace}}/downloads/install ${{github.workspace}}/ANTs/
 
+    - name: Integration tests
+      env:
+        DISPLAY: ':99.0'
+      run: |
+          cd ${{github.workspace}}
+          source tmp/venv/bin/activate
+          pip3 install pytest-qt pytest-cov
+          pytest --cov=gui --cov=utils ${{github.workspace}}/integration_tests
+          deactivate
+
     - name: Build software
       run: |
         cd ${{github.workspace}}
@@ -67,8 +77,8 @@ jobs:
     - name: Make installer
       run: |
         git clone https://github.com/dbouget/quickpkg.git
-        quickpkg/quickpkg dist/Raidionics.app --output Raidionics-1.2.4-macOS.pkg
-        cp -r Raidionics-1.2.4-macOS.pkg dist/Raidionics-1.2.4-macOS-arm64.pkg
+        quickpkg/quickpkg dist/Raidionics.app --output Raidionics-1.3.0-macOS.pkg
+        cp -r Raidionics-1.3.0-macOS.pkg dist/Raidionics-1.3.0-macOS-arm64.pkg
 
     - name: Upload package
       uses: actions/upload-artifact@v4

.github/workflows/build_ubuntu.yml

@@ -77,6 +77,14 @@ jobs:
         pip uninstall -y PySide6 PySide6-Addons PySide6-Essentials
         pip install --force-reinstall --no-cache-dir pyside6==6.2.4
 
+    - name: Integration tests
+      env:
+        DISPLAY: ':99.0'
+      run: |
+          pip install pytest-qt pytest-cov
+          /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX
+          pytest --cov=gui --cov=utils ${{github.workspace}}/integration_tests --cov-report=xml
+
     - name: Build software
       run: |
         pip install pyinstaller==5.13.2
@@ -108,11 +116,17 @@ jobs:
         cp -r dist/Raidionics assets/Raidionics_ubuntu/usr/local/bin
         dpkg-deb --build --root-owner-group assets/Raidionics_ubuntu
         ls -la
-        cp -r assets/Raidionics_ubuntu.deb dist/Raidionics-1.2.4-ubuntu.deb
+        cp -r assets/Raidionics_ubuntu.deb dist/Raidionics-1.3.0-ubuntu.deb
 
     - name: Upload package
       uses: actions/upload-artifact@v4
       with:
         name: Package
         path: ${{github.workspace}}/dist/Raidionics-*
-        if-no-files-found: error
+        if-no-files-found: error
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true

.github/workflows/build_windows.yml

@@ -46,6 +46,13 @@ jobs:
         pip install matplotlib==3.3.4
         pip install --force-reinstall --no-cache-dir pyside6
 
+#    - name: Integration tests
+#      env:
+#        DISPLAY: ':99.0'
+#      run: |
+#          pip install pytest-qt pytest-cov
+#          pytest --cov=gui --cov=utils ${{github.workspace}}/integration_tests
+
     - name: Build software
       run: |              
         pip install pyinstaller==5.13.2
@@ -62,7 +69,7 @@ jobs:
     - name: Make installer
       run: |
         makensis.exe assets/Raidionics.nsi
-        cp -r assets/Raidionics-1.2.4-win.exe dist/Raidionics-1.2.4-win.exe
+        cp -r assets/Raidionics-1.3.0-win.exe dist/Raidionics-1.3.0-win.exe
 
     - name: Upload package
       uses: actions/upload-artifact@v4

.gitignore

@@ -37,3 +37,4 @@ quickpkg/
 *.zip
 *.tar.gz
 assets/Raidionics_ubuntu/usr/local/bin
+.coverage

assets/Raidionics.nsi

@@ -1,8 +1,8 @@
 !define APP_NAME "Raidionics"
 !define COMP_NAME "SINTEF"
-!define VERSION "1.2.2"
+!define VERSION "1.3.0"
 !define DESCRIPTION "Application"
-!define INSTALLER_NAME "Raidionics-1.2.4-win.exe"
+!define INSTALLER_NAME "Raidionics-1.3.0-win.exe"
 !define MAIN_APP_EXE "Raidionics.exe"
 !define INSTALL_TYPE "SetShellVarContext current"
 !define REG_ROOT "HKLM"

assets/Raidionics_ubuntu/DEBIAN/control

@@ -1,5 +1,5 @@
 Package: Raidionics
-Version: 1.2.2
+Version: 1.3.0
 Architecture: i386
 Maintainer: David Bouget <david.bouget@sintef.no>
 Description: Raidionics—Reporting and Data System.

assets/main.spec

@@ -85,7 +85,7 @@ if sys.platform == "darwin":
                     'CFBundleIdentifier': 'Raidionics',
                     'CFBundleInfoDictionaryVersion': '6.0',
                     'CFBundleName': 'Raidionics',
-                    'CFBundleVersion': '1.2.4',
+                    'CFBundleVersion': '1.3.0',
                     'CFBundlePackageType': 'APPL',
                     'LSBackgroundOnly': 'false',
                 },

assets/main_arm.spec

@@ -84,7 +84,7 @@ if sys.platform == "darwin":
                     'CFBundleIdentifier': 'Raidionics',
                     'CFBundleInfoDictionaryVersion': '6.0',
                     'CFBundleName': 'Raidionics',
-                    'CFBundleVersion': '1.2.4',
+                    'CFBundleVersion': '1.3.0',
                     'CFBundlePackageType': 'APPL',
                     'LSBackgroundOnly': 'false',
                 },

gui/RaidionicsMainWindow.py

@@ -46,13 +46,15 @@ class RaidionicsMainWindow(QMainWindow):
     reload_interface = Signal()
     new_patient_clicked = Signal(str)  # Internal unique_id of the clicked patient
 
-    def __init__(self, application, *args, **kwargs):
+    def __init__(self, application=None, *args, **kwargs):
         super(RaidionicsMainWindow, self).__init__(*args, **kwargs)
 
-        self.app = application
-        self.app.setWindowIcon(QIcon(os.path.join(os.path.dirname(os.path.realpath(__file__)),
-                                                  'Images/raidionics-icon.png')))
-        self.app.setStyle("Fusion")  # @TODO: Should we remove Fusion style? Looks strange on macOS
+        self.app = None
+        if application is not None:
+            self.app = application
+            self.app.setWindowIcon(QIcon(os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                                                      'Images/raidionics-icon.png')))
+            self.app.setStyle("Fusion")  # @TODO: Should we remove Fusion style? Looks strange on macOS
         self.logs_thread = LogReaderThread()
         self.logs_thread.start()
         self.__set_interface()
@@ -70,9 +72,11 @@ def closeEvent(self, event):
                 and SoftwareConfigResources.getInstance().get_active_patient_uid() \
                 and SoftwareConfigResources.getInstance().get_active_patient().has_unsaved_changes():
             dialog = SavePatientChangesDialog()
-            code = dialog.exec_()
+            code = dialog.exec()
             if code == 0:  # Operation cancelled
                 event.ignore()
+        if self.logs_thread.isRunning():
+            self.logs_thread.stop()
         logging.info("Graceful exit.")
 
     def resizeEvent(self, event):
@@ -86,11 +90,14 @@ def __on_exit_software(self) -> None:
         """
         Mirroring of the closeEvent, for when the user press the Quit action in the main menu.
         """
-        self.logs_thread.stop()
+        if self.logs_thread.isRunning():
+            self.logs_thread.stop()
+
         if not SoftwareConfigResources.getInstance().is_patient_list_empty()\
+                and SoftwareConfigResources.getInstance().get_active_patient() is not None\
                 and SoftwareConfigResources.getInstance().get_active_patient().has_unsaved_changes():
             dialog = SavePatientChangesDialog()
-            code = dialog.exec_()
+            code = dialog.exec()
             if code == 1:  # Operation approved
                 logging.info("Graceful exit.")
                 sys.exit()
@@ -123,6 +130,10 @@ def __set_mainmenu_interface(self):
                                                                        'Images/download-tray-icon.png')),
                                                     'Download test data', self)
         self.file_menu.addAction(self.download_example_data_action)
+        self.clear_scene_action = QAction(QIcon(os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                                                      'Images/trash-bin_icon.png')), 'Clear', self)
+        self.file_menu.addAction(self.clear_scene_action)
+
         self.quit_action = QAction(QIcon(os.path.join(os.path.dirname(os.path.realpath(__file__)),
                                                       'Images/power-icon.png')), 'Quit', self)
         self.quit_action.setShortcut("Ctrl+Q")
@@ -360,12 +371,16 @@ def __set_menubar_connections(self):
         self.batch_mode_action.triggered.connect(self.__on_study_batch_clicked)
         self.settings_preferences_action.triggered.connect(self.__on_settings_preferences_clicked)
         # self.quit_action.triggered.connect(sys.exit)
+        self.clear_scene_action.triggered.connect(self.on_clear_scene)
         self.quit_action.triggered.connect(self.__on_exit_software)
         self.download_example_data_action.triggered.connect(self.__on_download_example_data)
 
     def __get_screen_dimensions(self):
-        screen = self.app.primaryScreen()
-        self.primary_screen_dimensions = screen.size()
+        if self.app is None:
+            self.primary_screen_dimensions = QSize(1200, 700)
+        else:
+            screen = self.app.primaryScreen()
+            self.primary_screen_dimensions = screen.size()
         logging.debug("Detected primary screen size [w: {}, h: {}]".format(self.primary_screen_dimensions.width(),
                                                                            self.primary_screen_dimensions.height()))
 
@@ -439,7 +454,7 @@ def __on_study_batch_clicked(self):
     def __on_settings_preferences_clicked(self):
         patient_space = UserPreferencesStructure.getInstance().display_space
         diag = SoftwareSettingsDialog(self)
-        diag.exec_()
+        diag.exec()
 
         # Reloading the interface is mainly meant to perform a visual refreshment based on the latest user display choices
         # For now: changing the display space for viewing a patient images.
@@ -464,11 +479,11 @@ def __on_patient_selected(self, patient_uid: str) -> None:
 
     def __on_community_action_triggered(self):
         popup = ResearchCommunityDialog(self)
-        popup.exec_()
+        popup.exec()
 
     def __on_about_action_triggered(self):
         popup = AboutDialog()
-        popup.exec_()
+        popup.exec()
 
     def __on_help_action_triggered(self) -> None:
         """
@@ -484,11 +499,11 @@ def __on_view_logs_triggered(self) -> None:
         Opens up a pop-up dialog allowing to read through the log file.
         """
         diag = LogsViewerDialog(self)
-        diag.exec_()
+        diag.exec()
 
     def __on_shortcuts_action_triggered(self):
         popup = KeyboardShortcutsDialog(self)
-        popup.exec_()
+        popup.exec()
 
     def __on_save_file_triggered(self):
         if SoftwareConfigResources.getInstance().get_active_patient_uid() \
@@ -499,7 +514,7 @@ def __on_save_file_triggered(self):
             SoftwareConfigResources.getInstance().get_active_study().save()
 
     def __on_download_example_data(self):
-        QDesktopServices.openUrl(QUrl("https://drive.google.com/file/d/1W3klW_F7Rfge9-utczz9qp7uWh-pVPS1/view?usp=sharing"))
+        QDesktopServices.openUrl(QUrl("https://github.com/raidionics/Raidionics-models/releases/download/v1.3.0-rc/Samples-Raidionics-ApprovedExample-v1.3.zip"))
 
     def on_process_log_message(self, log_msg: str) -> None:
         """
@@ -510,7 +525,7 @@ def on_process_log_message(self, log_msg: str) -> None:
         if True in [x in log_msg for x in cases]:
             diag = QErrorMessage(self)
             diag.setWindowTitle("Error or warning identified!")
-            diag.showMessage(log_msg + "\nPlease visit the log file (Settings > Logs)")
+            diag.showMessage(log_msg + "<br><br>Please visit the log file (Settings > Logs)")
             diag.setMinimumSize(QSize(400, 150))
             diag.exec()
 
@@ -523,3 +538,11 @@ def standardOutputWritten(self, text):
             # self.singleuse_mode_widget.standardOutputWritten(text)
         elif self.central_stackedwidget.currentIndex() == 2:
             self.batch_mode_widget.standardOutputWritten(text)
+
+    def on_clear_scene(self):
+        logging.info("[RaidionicsMainWindow] Interface clean-up. Removing all loaded patients and studies.")
+        self.batch_study_widget.on_clear_scene()
+        self.single_patient_widget.on_clear_scene()
+        SoftwareConfigResources.getInstance().reset() # <= Necessary for the integration tests not to crash...
+        if len(list(SoftwareConfigResources.getInstance().patients_parameters.keys())) > 0:
+            raise ValueError("[Software error] Existing patient IDs after clearing the scene!")

gui/SinglePatientComponent/CentralAreaExecutionWidget.py

@@ -34,6 +34,7 @@ def __init__(self, parent=None):
         super(CentralAreaExecutionWidget, self).__init__()
         self.parent = parent
         self.widget_name = "central_area_execution_widget"
+        self._tumor_type_diag = TumorTypeSelectionQDialog(self)
         self.__set_interface()
         self.__set_layout_dimensions()
         self.__set_stylesheets()
@@ -147,33 +148,31 @@ def on_pipeline_execution(self, pipeline_code: str) -> None:
         """
         self.model_name = ""
         if ("Classification" not in pipeline_code) and ("Brain" not in pipeline_code) and ("postop" not in pipeline_code) and ("Edema" not in pipeline_code) and ("Cavity" not in pipeline_code):
-            diag = TumorTypeSelectionQDialog(self)
-            code = diag.exec_()
+            code = self._tumor_type_diag.exec()
             if code == 0:  # Operation cancelled
                 return
 
-            if diag.tumor_type == 'Glioblastoma':
+            if self._tumor_type_diag.tumor_type == 'Glioblastoma':
                 self.model_name = "MRI_GBM"
-            elif diag.tumor_type == 'Low-Grade Glioma':
+            elif self._tumor_type_diag.tumor_type == 'Low-Grade Glioma':
                 self.model_name = "MRI_LGGlioma"
-            elif diag.tumor_type == 'Metastasis':
+            elif self._tumor_type_diag.tumor_type == 'Metastasis':
                 self.model_name = "MRI_Metastasis"
-            elif diag.tumor_type == 'Meningioma':
+            elif self._tumor_type_diag.tumor_type == 'Meningioma':
                 self.model_name = "MRI_Meningioma"
 
             if UserPreferencesStructure.getInstance().segmentation_tumor_model_type != "Tumor":
                 self.model_name = self.model_name + '_multiclass'
-                if diag.tumor_type == 'Low-Grade Glioma':
+                if self._tumor_type_diag.tumor_type == 'Low-Grade Glioma':
                     self.model_name = "MRI_GBM_multiclass"
         elif "postop" in pipeline_code:
-            diag = TumorTypeSelectionQDialog(self)
-            code = diag.exec_()
+            code = self._tumor_type_diag.exec()
             if code == 0:  # Operation cancelled
                 return
-            if diag.tumor_type == 'Glioblastoma':
+            if self._tumor_type_diag.tumor_type == 'Glioblastoma':
                 self.model_name = "MRI_GBM_Postop_FV_4p"
                 pipeline_code = pipeline_code + '_GBM'
-            elif diag.tumor_type == 'Low-Grade Glioma':
+            elif self._tumor_type_diag.tumor_type == 'Low-Grade Glioma':
                 self.model_name = "MRI_LGGlioma_Postop"
                 pipeline_code = pipeline_code + '_LGGlioma'
         elif "Brain" in pipeline_code:
@@ -258,7 +257,7 @@ def assertion_input_compatible(self, tumor_type: str) -> bool:
                 color: rgba(0, 0, 0, 1);
                 background-color: rgba(255, 255, 255, 1);
                 }""")
-                box.exec_()
+                box.exec()
                 return False
         else:
             valid_ids = SoftwareConfigResources.getInstance().get_active_patient().get_all_mri_volumes_for_sequence_type(MRISequenceType.FLAIR)
@@ -273,7 +272,7 @@ def assertion_input_compatible(self, tumor_type: str) -> bool:
                 color: rgba(0, 0, 0, 1);
                 background-color: rgba(255, 255, 255, 1);
                 }""")
-                box.exec_()
+                box.exec()
                 return False
 
         return True

gui/SinglePatientComponent/CentralDisplayArea/CustomQGraphicsView.py

@@ -178,7 +178,7 @@ def dropEvent(self, event):
         dialog.patient_imported.connect(self.patient_imported)
 
         dialog.setup_interface_from_files(entered_eligible_files)
-        code = dialog.exec_()
+        code = dialog.exec()
 
         # if code == QDialog.Accepted:
 

gui/SinglePatientComponent/LayersInteractorSidePanel/AnnotationLayersInteractor/AnnotationSingleLayerWidget.py

@@ -488,7 +488,7 @@ def adjustSize(self):
         self.resizeRequested.emit()
 
     def on_options_clicked(self, point):
-        self.options_menu.exec_(self.options_pushbutton.mapToGlobal(QPoint(0, 0)))
+        self.options_menu.exec(self.options_pushbutton.mapToGlobal(QPoint(0, 0)))
 
     def on_advanced_options_clicked(self):
         self.adjustSize()
@@ -521,7 +521,7 @@ def __on_opacity_changed(self, value):
         self.opacity_value_changed.emit(self.uid, value)
 
     def __on_color_selector_clicked(self):
-        code = self.color_dialog.exec_()
+        code = self.color_dialog.exec()
         if code == QColorDialog.Accepted:
             color = self.color_dialog.currentColor()
             self.color_value_changed.emit(self.uid, color)