Integration tests for data loading + CI attempt[skip ci]

.github/workflows/build_ubuntu.yml

@@ -102,6 +102,13 @@ jobs:
           export QT_QPA_PLATFORM="offscreen"
           cd ${{github.workspace}}/tests && python software_launch_test.py
 
+    - name: Integration tests
+      env:
+        DISPLAY: ':1'
+      run: |
+          pip install pytest
+          pytest ${{github.workspace}}/integration_tests
+
     - name: Make installer
       run: |
         mkdir -p assets/Raidionics_ubuntu/usr/local/bin

gui/SinglePatientComponent/LayersInteractorSidePanel/MRIVolumesInteractor/MRISeriesLayerWidget.py

@@ -107,7 +107,7 @@ def __set_layout_dimensions(self):
         # logging.debug("MRISeriesLayerWidget size set to {}.\n".format(self.size()))
 
     def __set_connections(self):
-        self.display_name_lineedit.textEdited.connect(self.on_name_change)
+        self.display_name_lineedit.returnPressed.connect(self.on_name_change)
         self.display_toggle_radiobutton.toggled.connect(self.on_visibility_toggled)
         self.options_pushbutton.clicked.connect(self.on_options_clicked)
         self.sequence_type_combobox.currentTextChanged.connect(self.on_sequence_type_changed)
@@ -343,10 +343,11 @@ def on_visibility_toggled(self, state):
         self.contrast_adjuster_pushbutton.setEnabled(self.display_toggle_radiobutton.isChecked())
         logging.info("[MRISeriesLayerWidget] Visibility toggled to {} for {}".format(state, self.uid))
 
-    def on_name_change(self, text):
+    def on_name_change(self):
         # @TODO. Should there be a check that the name is available?
-        SoftwareConfigResources.getInstance().get_active_patient().get_mri_by_uid(self.uid).display_name = text
-        self.display_name_changed.emit(self.uid, text)
+        new_name = self.display_name_lineedit.text()
+        SoftwareConfigResources.getInstance().get_active_patient().get_mri_by_uid(self.uid).display_name = new_name
+        self.display_name_changed.emit(self.uid, new_name)
 
     def on_sequence_type_changed(self, text) -> None:
         SoftwareConfigResources.getInstance().get_active_patient().get_mri_by_uid(self.uid).set_sequence_type(text)

gui/SinglePatientComponent/PatientResultsSidePanel/TumorCharacteristicsWidget.py

@@ -793,7 +793,7 @@ def populate_from_report(self) -> None:
 
         # BrainGrid structures
         self.braingridstructures_collapsiblegroupbox.clear_content_layout()
-        if UserPreferencesStructure.getInstance().compute_braingrid_structures:
+        if 'BrainGrid' in list(report_json['Main']['Total'].keys()): #UserPreferencesStructure.getInstance().compute_braingrid_structures:
             lay = QHBoxLayout()
             label_header = QLabel("Infiltration count:")
             label_header.setStyleSheet("""

gui/UtilsWidgets/CustomQDialog/ImportFoldersQDialog.py

@@ -192,6 +192,7 @@ def __on_exit_accept_clicked(self) -> None:
         self.load_progressbar.setValue(0)
 
         for input_folderpath in input_folderpaths:
+            logging.debug("[ImportFoldersQDialog] Parsing the current folder input with value: {}".format(input_folderpath))
             try:
                 folders_in_path = []
 

integration_tests/patient_loading_test.py

@@ -0,0 +1,132 @@
+import os
+import shutil
+from time import sleep
+
+import requests
+import zipfile
+
+import pytest
+from PySide6.QtCore import Qt
+
+from gui.RaidionicsMainWindow import RaidionicsMainWindow
+from gui.UtilsWidgets.CustomQDialog.ImportDataQDialog import ImportDataQDialog
+from gui.UtilsWidgets.CustomQDialog.ImportFoldersQDialog import ImportFolderLineWidget
+from utils.software_config import SoftwareConfigResources
+from utils.data_structures.UserPreferencesStructure import UserPreferencesStructure
+
+
+def_loc = UserPreferencesStructure.getInstance().user_home_location
+
+@pytest.fixture
+def test_location():
+    test_loc = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'integrationtests')
+    UserPreferencesStructure.getInstance().user_home_location = test_loc
+    if os.path.exists(test_loc):
+        shutil.rmtree(test_loc)
+    os.makedirs(test_loc)
+    return test_loc
+
+@pytest.fixture
+def test_data_folder():
+    test_data_url = 'https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Samples-Raidionics-ApprovedExample-v1.2.zip'
+    test_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'integrationtests')
+    test_data_dir = os.path.join(test_dir, 'ApprovedExample')
+    if os.path.exists(test_data_dir) and len(os.listdir(test_data_dir)) > 0:
+        return test_data_dir
+
+    archive_dl_dest = os.path.join(test_dir, 'raidionics_resources.zip')
+    headers = {}
+    response = requests.get(test_data_url, headers=headers, stream=True)
+    response.raise_for_status()
+    if response.status_code == requests.codes.ok:
+        with open(archive_dl_dest, "wb") as f:
+            for chunk in response.iter_content(chunk_size=1048576):
+                f.write(chunk)
+    with zipfile.ZipFile(archive_dl_dest, 'r') as zip_ref:
+        zip_ref.extractall(test_dir)
+    return test_data_dir
+
+
+@pytest.fixture
+def window():
+    """
+
+    """
+    window = RaidionicsMainWindow()
+    return window
+
+
+def test_patient_loading_from_files(qtbot, test_location, test_data_folder, window):
+    """
+
+    """
+    qtbot.addWidget(window)
+    # Entering the single patient widget view
+    qtbot.mouseClick(window.welcome_widget.left_panel_single_patient_pushbutton, Qt.MouseButton.LeftButton)
+
+    # Importing MRI files from Import patient > Other data type (*.nii)
+    # window.single_patient_widget.results_panel.add_other_data_action.trigger() <= Cannot use the actual pushbutton action as it would open the QDialog...
+    window.single_patient_widget.results_panel.on_add_new_empty_patient()
+    t1_sample_mri_filename = os.path.join(test_data_folder, 'Raw', 'Case27-T1.nii.gz')
+    flair_sample_mri_filename = os.path.join(test_data_folder, 'Raw', 'Case27-FLAIR.nii.gz')
+    window.single_patient_widget.import_data_dialog.setup_interface_from_files([t1_sample_mri_filename, flair_sample_mri_filename])
+    window.single_patient_widget.import_data_dialog.__on_exit_accept_clicked()
+    assert len(list(SoftwareConfigResources.getInstance().get_active_patient().mri_volumes.keys())) == 2
+
+    # Saving the latest modifications to the patient on disk by pressing the disk icon
+    qtbot.mouseClick(window.single_patient_widget.results_panel.patient_results_widgets[
+                       list(window.single_patient_widget.results_panel.patient_results_widgets.keys())[0]].save_patient_pushbutton, Qt.MouseButton.LeftButton)
+
+def test_patient_loading_from_folder(qtbot, test_location, test_data_folder, window):
+    """
+
+    """
+    qtbot.addWidget(window)
+    # Entering the single patient widget view
+    qtbot.mouseClick(window.welcome_widget.left_panel_single_patient_pushbutton, Qt.MouseButton.LeftButton)
+
+    # Importing MRI files from Import patient > Other data type (*.nii)
+    # window.single_patient_widget.results_panel.add_folder_data_action.trigger() <= Cannot use the actual pushbutton action as it would open the QDialog...
+    window.single_patient_widget.results_panel.on_add_new_empty_patient()
+    sample_folder = os.path.join(test_data_folder, 'Raw')
+
+    window.single_patient_widget.import_folder_dialog.reset()
+    window.single_patient_widget.import_folder_dialog.set_parsing_mode("single")
+    window.single_patient_widget.import_folder_dialog.set_target_type("regular")
+    wid = ImportFolderLineWidget()
+    wid.filepath_lineedit.setText(sample_folder)
+    window.single_patient_widget.import_folder_dialog.import_scrollarea_layout.insertWidget(window.single_patient_widget.import_folder_dialog.import_scrollarea_layout.count() - 1, wid)
+    window.single_patient_widget.import_folder_dialog.__on_exit_accept_clicked()
+    assert len(list(SoftwareConfigResources.getInstance().get_patient_by_display_name("Raw").mri_volumes.keys())) == 2
+
+    # Saving the latest modifications to the patient on disk by pressing the disk icon
+    qtbot.mouseClick(window.single_patient_widget.results_panel.patient_results_widgets[
+                       list(window.single_patient_widget.results_panel.patient_results_widgets.keys())[0]].save_patient_pushbutton, Qt.MouseButton.LeftButton)
+
+
+def test_patient_loading_from_raidionics(qtbot, test_location, test_data_folder, window):
+    """
+
+    """
+    qtbot.addWidget(window)
+    # Entering the single patient widget view
+    qtbot.mouseClick(window.welcome_widget.left_panel_single_patient_pushbutton, Qt.MouseButton.LeftButton)
+
+    # Importing MRI files from Import patient > Other data type (*.nii)
+    # window.single_patient_widget.results_panel.add_raidionics_patient_action.trigger() <= Cannot use the actual pushbutton action as it would open the QDialog...
+    raidionics_filename = os.path.join(test_data_folder, 'Raidionics', "patients", "patient_1", "patient_1_scene.raidionics")
+    window.single_patient_widget.import_data_dialog.reset()
+    window.single_patient_widget.import_data_dialog.set_parsing_filter("patient")
+    window.single_patient_widget.import_data_dialog.setup_interface_from_files([raidionics_filename])
+    window.single_patient_widget.import_data_dialog.__on_exit_accept_clicked()
+    assert len(list(SoftwareConfigResources.getInstance().get_patient_by_display_name("Patient 1").mri_volumes.keys())) == 2
+
+    # Saving the latest modifications to the patient on disk by pressing the disk icon
+    qtbot.mouseClick(window.single_patient_widget.results_panel.patient_results_widgets[
+                       list(window.single_patient_widget.results_panel.patient_results_widgets.keys())[0]].save_patient_pushbutton, Qt.MouseButton.LeftButton)
+
+def test_cleanup():
+    UserPreferencesStructure.getInstance().user_home_location = def_loc
+    test_loc = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'integrationtests')
+    if os.path.exists(test_loc):
+        shutil.rmtree(test_loc)

utils/data_structures/InvestigationTimestampStructure.py

@@ -105,17 +105,16 @@ def display_name(self, text: str) -> None:
             self._display_name = text
             new_folder_name = self._display_name.strip().replace(" ", "")
             if os.path.exists(os.path.join(self._output_patient_folder, new_folder_name)):
-                # @TODO. Should return an error message, but then should be made into a set_display_name method....
-                return
+                msg = 'A timestamp with requested name already exists in the destination folder.<br>' + \
+                      'Requested name: {}.<br>'.format(new_folder_name) + \
+                      'Destination folder: {}.'.format(os.path.dirname(self._output_patient_folder))
+                raise ValueError(msg)
             if os.path.exists(os.path.join(self._output_patient_folder, self._folder_name)):
                 shutil.move(src=os.path.join(self._output_patient_folder, self._folder_name),
                             dst=os.path.join(self._output_patient_folder, new_folder_name))
                 logging.debug(
                     "Unsaved changes - Investigation timestamp folder name changed from {} to {}".format(self._folder_name,
                                                                                                          new_folder_name))
-            else:
-                raise ValueError("Folder not existing on disk at: {}".format(os.path.join(self._output_patient_folder,
-                                                                                          self._folder_name)))
             self._folder_name = new_folder_name
             self._unsaved_changes = True
         except Exception as e:

utils/data_structures/PatientParametersStructure.py

@@ -394,9 +394,8 @@ def import_data(self, filename: str, investigation_ts: str = None, investigation
 
         Returns
         -------
-        data_uid, error_message: [str, str]
-            A tuple [str, str] containing first the new internal unique identifier for the loaded volume, and second
-            a potential error message.
+        data_uid: str
+            A string containing the new internal unique identifier for the loaded volume.
         """
         data_uid = None
 

utils/data_structures/ReportingStructure.py

@@ -45,21 +45,24 @@ class ReportingStructure:
 
     def __init__(self, uid: str, report_filename: str, output_patient_folder: str, inv_ts_uid: str,
                  inv_ts_folder_name: str = None, reload_params: dict = None) -> None:
-        self.__reset()
-        self._unique_id = uid
-        self._report_filename = report_filename
-        self._output_patient_folder = output_patient_folder
-        self._timestamp_uid = inv_ts_uid
-        if inv_ts_folder_name:
-            self._timestamp_folder_name = inv_ts_folder_name
-
-        with open(self._report_filename, 'r') as infile:
-            self._report_content = json.load(infile)
-
-        if reload_params:
-            self.__reload_from_disk(reload_params)
-        else:
-            self.__init_from_scratch()
+        try:
+            self.__reset()
+            self._unique_id = uid
+            self._report_filename = report_filename
+            self._output_patient_folder = output_patient_folder
+            self._timestamp_uid = inv_ts_uid
+            if inv_ts_folder_name:
+                self._timestamp_folder_name = inv_ts_folder_name
+
+            with open(self._report_filename, 'r') as infile:
+                self._report_content = json.load(infile)
+
+            if reload_params:
+                self.__reload_from_disk(reload_params)
+            else:
+                self.__init_from_scratch()
+        except Exception as e:
+            raise RuntimeError(e)
 
     def __reset(self):
         """
@@ -189,20 +192,23 @@ def __reload_from_disk(self, params: dict):
         """
 
         """
-        self._timestamp_uid = params['investigation_timestamp_uid']
-        if self._timestamp_uid:
-            self._timestamp_folder_name = params['report_filename'].split('/')[0]
-            if os.name == 'nt':
-                self._timestamp_folder_name = list(PurePath(params['report_filename']).parts)[0]
+        try:
+            self._timestamp_uid = params['investigation_timestamp_uid']
+            if self._timestamp_uid:
+                self._timestamp_folder_name = params['report_filename'].split('/')[0]
+                if os.name == 'nt':
+                    self._timestamp_folder_name = list(PurePath(params['report_filename']).parts)[0]
 
-        if 'parent_mri_uid' in list(params.keys()):
-            self._parent_mri_uid = params['parent_mri_uid']
+            if 'parent_mri_uid' in list(params.keys()):
+                self._parent_mri_uid = params['parent_mri_uid']
 
-        if 'task' in list(params.keys()):
-            self.set_reporting_type(params['task'])
+            if 'task' in list(params.keys()):
+                self.set_reporting_type(params['task'])
 
-        if 'report_filename_csv' in list(params.keys()):
-            self._report_filename_csv = os.path.join(self._output_patient_folder, params["report_filename_csv"])
+            if 'report_filename_csv' in list(params.keys()):
+                self._report_filename_csv = os.path.join(self._output_patient_folder, params["report_filename_csv"])
+        except Exception as e:
+            raise RuntimeError("""Reloading the reporting structure from disk failed for {} with {}.""".format(self.report_filename, e))
 
     def save(self) -> dict:
         """
@@ -227,5 +233,5 @@ def save(self) -> dict:
                 report_params['report_filename_csv'] = os.path.relpath(self._report_filename_csv, base_patient_folder)
             self._unsaved_changes = False
             return report_params
-        except Exception:
-            logging.error("[Software error] ReportingStructure saving failed with:\n {}".format(traceback.format_exc()))
+        except Exception as e:
+            logging.error("ReportingStructure saving failed with: {}".format(e))

utils/data_structures/StudyParametersStructure.py

@@ -38,17 +38,20 @@ def __init__(self, uid: str = "-1", dest_location: str = None, study_filename: s
         """
 
         """
-        self.__reset()
-        self._unique_id = uid.replace(" ", '_').strip()
+        try:
+            self.__reset()
+            self._unique_id = uid.replace(" ", '_').strip()
 
-        if study_filename:
-            # Empty init, self.import_study() must be called after the instance creation call.
-            pass
-        else:
-            if not dest_location:
-                logging.warning("Home folder location for new study creation is None.")
-                dest_location = os.path.join(os.path.expanduser('~'), '.raidionics')
-            self.__init_from_scratch(dest_location)
+            if study_filename:
+                # Empty init, self.import_study() must be called after the instance creation call.
+                pass
+            else:
+                if not dest_location:
+                    logging.warning("Home folder location for new study creation is None.")
+                    dest_location = os.path.join(os.path.expanduser('~'), '.raidionics')
+                self.__init_from_scratch(dest_location)
+        except Exception as e:
+            raise RuntimeError(e)
 
     def __reset(self):
         """