class Ui_ReactionEditDialog(object):
def setupUi(self, ReactionEditDialog):
ReactionEditDialog.setObjectName("ReactionEditDialog")
ReactionEditDialog.resize(383, 200)
self.verticalLayout = QtWidgets.QVBoxLayout(ReactionEditDialog)
self.verticalLayout.setObjectName("verticalLayout")
self.attributeWidget = ReactionAttributesDisplayWidget(ReactionEditDialog)
self.attributeWidget.setObjectName("attributeWidget")
self.verticalLayout.addWidget(self.attributeWidget)
self.tabWidget = QtWidgets.QTabWidget(ReactionEditDialog)
self.tabWidget.setTabShape(QtWidgets.QTabWidget.Rounded)
self.tabWidget.setObjectName("tabWidget")
self.metaboliteTab = StoichiometryDisplayWidget()
self.metaboliteTab.setObjectName("metaboliteTab")
self.horizontalLayout_2 = QtWidgets.QHBoxLayout(self.metaboliteTab)
self.horizontalLayout_2.setObjectName("horizontalLayout_2")
self.tabWidget.addTab(self.metaboliteTab, "")
self.geneTab = GenesDisplayWidget()
self.geneTab.setObjectName("geneTab")
self.verticalLayout_3 = QtWidgets.QVBoxLayout(self.geneTab)
self.verticalLayout_3.setObjectName("verticalLayout_3")
self.tabWidget.addTab(self.geneTab, "")
self.annotationTab = AnnotationDisplayWidget()
self.annotationTab.setObjectName("annotationTab")
self.horizontalLayout_4 = QtWidgets.QHBoxLayout(self.annotationTab)
self.horizontalLayout_4.setObjectName("horizontalLayout_4")
self.tabWidget.addTab(self.annotationTab, "")
self.evidenceTab = EvidenceDisplayWidget()
self.evidenceTab.setObjectName("evidenceTab")
self.horizontalLayout_5 = QtWidgets.QHBoxLayout(self.evidenceTab)
self.horizontalLayout_5.setObjectName("horizontalLayout_5")
self.tabWidget.addTab(self.evidenceTab, "")
self.commentTab = CommentDisplayWidget()
self.commentTab.setObjectName("commentTab")
self.verticalLayout_6 = QtWidgets.QVBoxLayout(self.commentTab)
self.verticalLayout_6.setObjectName("verticalLayout_6")
self.tabWidget.addTab(self.commentTab, "")
self.verticalLayout.addWidget(self.tabWidget)
self.buttonBox = QtWidgets.QDialogButtonBox(ReactionEditDialog)
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Save)
self.buttonBox.setObjectName("buttonBox")
self.verticalLayout.addWidget(self.buttonBox)
self.retranslateUi(ReactionEditDialog)
self.tabWidget.setCurrentIndex(0)
self.buttonBox.accepted.connect(ReactionEditDialog.accept)
self.buttonBox.rejected.connect(ReactionEditDialog.reject)
QtCore.QMetaObject.connectSlotsByName(ReactionEditDialog)
def retranslateUi(self, ReactionEditDialog):
_translate = QtCore.QCoreApplication.translate
ReactionEditDialog.setWindowTitle(_translate("ReactionEditDialog", "Edit reaction"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.metaboliteTab), _translate("ReactionEditDialog", "Metabolites"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.geneTab), _translate("ReactionEditDialog", "Genes"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.annotationTab), _translate("ReactionEditDialog", "Annotations"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.evidenceTab), _translate("ReactionEditDialog", "Evidence"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.commentTab), _translate("ReactionEditDialog", "Comment"))
class Ui_MetaboliteEditDialog(object):
def setupUi(self, MetaboliteEditDialog):
MetaboliteEditDialog.setObjectName("MetaboliteEditDialog")
MetaboliteEditDialog.resize(240, 223)
self.verticalLayout = QtWidgets.QVBoxLayout(MetaboliteEditDialog)
self.verticalLayout.setObjectName("verticalLayout")
self.attributeWidget = MetaboliteAttributesDisplayWidget(
MetaboliteEditDialog)
self.attributeWidget.setObjectName("attributeWidget")
self.verticalLayout.addWidget(self.attributeWidget)
self.tabWidget = QtWidgets.QTabWidget(MetaboliteEditDialog)
self.tabWidget.setObjectName("tabWidget")
self.reactionsTab = ReactionsDisplayWidget()
self.reactionsTab.setObjectName("reactionsTab")
self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.reactionsTab)
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.tabWidget.addTab(self.reactionsTab, "")
self.annotationTab = AnnotationDisplayWidget()
self.annotationTab.setObjectName("annotationTab")
self.verticalLayout_3 = QtWidgets.QVBoxLayout(self.annotationTab)
self.verticalLayout_3.setObjectName("verticalLayout_3")
self.tabWidget.addTab(self.annotationTab, "")
self.evidenceTab = EvidenceDisplayWidget()
self.evidenceTab.setObjectName("evidenceTab")
self.verticalLayout_4 = QtWidgets.QVBoxLayout(self.evidenceTab)
self.verticalLayout_4.setObjectName("verticalLayout_4")
self.tabWidget.addTab(self.evidenceTab, "")
self.verticalLayout.addWidget(self.tabWidget)
self.buttonBox = QtWidgets.QDialogButtonBox(MetaboliteEditDialog)
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel
| QtWidgets.QDialogButtonBox.Save)
self.buttonBox.setObjectName("buttonBox")
self.verticalLayout.addWidget(self.buttonBox)
self.retranslateUi(MetaboliteEditDialog)
self.tabWidget.setCurrentIndex(0)
self.buttonBox.accepted.connect(MetaboliteEditDialog.accept)
self.buttonBox.rejected.connect(MetaboliteEditDialog.reject)
QtCore.QMetaObject.connectSlotsByName(MetaboliteEditDialog)
def retranslateUi(self, MetaboliteEditDialog):
_translate = QtCore.QCoreApplication.translate
MetaboliteEditDialog.setWindowTitle(
_translate("MetaboliteEditDialog", "Edit metabolite"))
self.tabWidget.setTabText(
self.tabWidget.indexOf(self.reactionsTab),
_translate("MetaboliteEditDialog", "Reactions"))
self.tabWidget.setTabText(
self.tabWidget.indexOf(self.annotationTab),
_translate("MetaboliteEditDialog", "Annotation"))
self.tabWidget.setTabText(
self.tabWidget.indexOf(self.evidenceTab),
_translate("MetaboliteEditDialog", "Evidence"))
def test_changed_triggered_addition(self):
widget = EvidenceDisplayWidget()
reaction = Reaction()
model = Model()
widget.set_item(reaction, model)
mock = Mock()
widget.changed.connect(mock.test)
assert mock.test.called is False
assert widget.dataTable.rowCount() == 0
QtTest.QTest.mouseClick(widget.add_button, QtCore.Qt.LeftButton)
assert widget.dataTable.rowCount() == 1
assert mock.test.called is True
def test_set_item(self):
widget = EvidenceDisplayWidget()
evidence = Evidence()
reaction = Reaction()
model = Model()
evidence.set_entity(reaction)
widget.set_item(reaction, model)
# Check that a copy of the evidence has been added to the table
assert widget.dataTable.rowCount() == 1
assert widget.dataTable.item(0).link is not evidence
assert widget.dataTable.item(
0).link.internal_id == evidence.internal_id
def test_changed_triggered_deletion(self):
widget = EvidenceDisplayWidget()
evidence = Evidence()
reaction = Reaction()
model = Model()
evidence.set_entity(reaction)
widget.set_item(reaction, model)
mock = Mock()
widget.changed.connect(mock.test)
assert mock.test.called is False
assert widget.dataTable.rowCount() == 1
widget.dataView.selectRow(0)
QtTest.QTest.mouseClick(widget.delete_button, QtCore.Qt.LeftButton)
assert widget.dataTable.rowCount() == 0
assert mock.test.called is True
def test_setup(self):
widget = EvidenceDisplayWidget()
assert widget.dataTable.rowCount() == 0
assert widget.item is None
assert widget.model is None
assert widget.dataView.model() is widget.dataTable
assert widget.content_changed is False
def setupUi(self, GeneEditDialog):
GeneEditDialog.setObjectName("GeneEditDialog")
GeneEditDialog.resize(260, 182)
self.verticalLayout = QtWidgets.QVBoxLayout(GeneEditDialog)
self.verticalLayout.setObjectName("verticalLayout")
self.attributeWidget = GeneAttributesDisplayWidget(GeneEditDialog)
self.attributeWidget.setObjectName("attributeWidget")
self.verticalLayout.addWidget(self.attributeWidget)
self.tabWidget = QtWidgets.QTabWidget(GeneEditDialog)
self.tabWidget.setObjectName("tabWidget")
self.reactionTab = ReactionsDisplayWidget()
self.reactionTab.setObjectName("reactionTab")
self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.reactionTab)
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.tabWidget.addTab(self.reactionTab, "")
self.tab_annotations = AnnotationDisplayWidget()
self.tab_annotations.setObjectName("tab_annotations")
self.verticalLayout_3 = QtWidgets.QVBoxLayout(self.tab_annotations)
self.verticalLayout_3.setObjectName("verticalLayout_3")
self.tabWidget.addTab(self.tab_annotations, "")
self.evidenceTab = EvidenceDisplayWidget()
self.evidenceTab.setObjectName("evidenceTab")
self.tabWidget.addTab(self.evidenceTab, "")
self.verticalLayout.addWidget(self.tabWidget)
self.buttonBox = QtWidgets.QDialogButtonBox(GeneEditDialog)
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel
| QtWidgets.QDialogButtonBox.Save)
self.buttonBox.setObjectName("buttonBox")
self.verticalLayout.addWidget(self.buttonBox)
self.retranslateUi(GeneEditDialog)
self.tabWidget.setCurrentIndex(0)
self.buttonBox.accepted.connect(GeneEditDialog.accept)
self.buttonBox.rejected.connect(GeneEditDialog.reject)
QtCore.QMetaObject.connectSlotsByName(GeneEditDialog)
def test_saving_changes(self):
reaction = Reaction()
reference = Reference()
model = Model()
evidence = Evidence(entity=reaction)
evidence.add_reference(reference)
widget = EvidenceDisplayWidget()
model.all_evidences[evidence.internal_id] = evidence
assert evidence in reaction.evidences
assert evidence.internal_id in model.all_evidences
assert reference in evidence.references
# Set reaction and model to widget
widget.set_item(reaction, model)
assert widget.dataTable.rowCount() == 1
# Remove evidence copy from data table
widget.dataTable.setRowCount(0)
# Setup new evidence item
new_evidence = Evidence()
new_evidence.assertion = "Catalyzed by"
new_evidence.entity = reaction
reference = Reference()
new_evidence.add_reference(reference, reciprocal=False)
# Test the setup i.e. that items are only linked in a one way (evidence -> item) fashion
assert new_evidence not in reaction.evidences
assert new_evidence not in reference.linked_items
# Add new reference to widget table
widget.dataTable.update_row_from_item(new_evidence)
assert widget.dataTable.rowCount() == 1
assert widget.dataTable.item(0).link is new_evidence
# Action - Save evidences
widget.save_state()
# Check that old instance is detached from all links
assert evidence not in reaction.evidences
assert len(evidence.references) == 0
# Old evidence still kept alive by this test
old_id = evidence.internal_id
assert old_id in model.all_evidences
evidence = None
gc.collect()
assert old_id not in model.all_evidences
# Check that new evidence is linked properly
assert new_evidence in reaction.evidences
assert new_evidence.internal_id in model.all_evidences
def test_changed_triggered_edition(self):
widget = EvidenceDisplayWidget()
evidence = Evidence()
reaction = Reaction()
model = Model()
evidence.set_entity(reaction)
reaction.add_evidence(evidence)
widget.set_item(reaction, model)
mock = Mock()
widget.changed.connect(mock.test)
assert mock.test.called is False
assert widget.dataTable.rowCount() == 1
widget.dataView.selectRow(0)
widget.edit_item()
assert widget.dataTable.rowCount() == 1
assert mock.test.called is True