properly close HDF5 filles and percussions for opening.

src/PyMca5/PyMcaCore/NexusDataSource.py

@@ -227,6 +227,15 @@ def refresh(self):
             phynxInstance._sourceName = pattern
         self.__lastKeyInfo = {}
 
+    def close(self):
+        """Close every open HDF5 handle held by this source."""
+        for instance in self._sourceObjectList:
+            try:
+                instance.close()
+            except Exception as e:
+                _logger.debug("Error closing HDF5 source: %s", e)
+        self._sourceObjectList = []
+
     def getSourceInfo(self):
         """
         Returns a dictionary with the key "KeyList" (list of all available keys

src/PyMca5/PyMcaGui/io/hdf5/HDF5Widget.py

@@ -425,11 +425,14 @@ class FileModel(qt.QAbstractItemModel):
     """
     sigFileUpdated = qt.pyqtSignal(object)
     sigFileAppended = qt.pyqtSignal(object)
+    sigReadFailed = qt.pyqtSignal(object)
 
     def __init__(self, parent=None):
         qt.QAbstractItemModel.__init__(self, parent)
         self.rootItem = RootItem(['File/Group/Dataset', 'Description', 'Shape', 'DType'])
         self._idMap = {qt.QModelIndex().internalId(): self.rootItem}
+        # to warn only once about read error, can be reset intentionally
+        self._readErrorReported = False
 
     def sort(self, column, order):
         #print("FileModel sort called with ", column, order)
@@ -572,7 +575,14 @@ def parent(self, index):
             return self.createIndex(parent.row, 0, parent)
 
     def rowCount(self, index):
-        return len(self.getProxyFromIndex(index))
+        try:
+            # the `len(self.children)` can fail.
+            return len(self.getProxyFromIndex(index))
+        except Exception:
+            if not self._readErrorReported:
+                self._readErrorReported = True
+                self.sigReadFailed.emit({"event": "readError", "index": index})
+            return 0
 
     def openFile(self, filename, weakreference=False):
         gc.collect()

src/PyMca5/PyMcaGui/io/hdf5/QNexusWidget.py

@@ -492,6 +492,7 @@ def dataSourceDestroyed(weakrefReference):
         # stays visible and the tree does not collapse.
         try:
             newModel = HDF5Widget.FileModel()
+            newModel.sigReadFailed.connect(self._hdf5ReadFailed)
             for source in self.data._sourceObjectList:
                 newModel.appendPhynxFile(source, weakreference=True)
             self._modelDict[ref] = newModel
@@ -515,6 +516,32 @@ def dataSourceDestroyed(weakrefReference):
             if hasattr(self.hdf5Widget, "expandToDepth"):
                 self.hdf5Widget.expandToDepth(0)
 
+    def _hdf5ReadFailed(self, ddict):
+        self._recoverFromReadError(ddict.get("index"))
+        self._showReadFailedMessage()
+
+    def _recoverFromReadError(self, index):
+        model = self.hdf5Widget.model()
+        # Collapse the node that failed to be read
+        if index is not None and index.isValid():
+            self.hdf5Widget.collapse(index)
+        # A later failed expansion should warn again
+        if hasattr(model, "_readErrorReported"):
+            model._readErrorReported = False
+
+    def _showReadFailedMessage(self):
+        msg = qt.QMessageBox(self)
+        msg.setIcon(qt.QMessageBox.Warning)
+        msg.setWindowTitle("Cannot read HDF5 file")
+        msg.setText("The selected file could not be read.")
+        msg.setInformativeText(
+            "It may be being written now. Try again later." \
+            "If it is stuck, try to refresh (F5) or close and open the file again.")
+        # `open()` (not `exec()`) blocks the window but not the code
+        # `WA_DeleteOnClose` to delete itself on close (to avoid a leak)
+        msg.setAttribute(qt.Qt.WA_DeleteOnClose)
+        msg.open()
+
     def _autoRefreshDatasets(self, source=None, moveToLastSlice=True):
         """
         Auto-refresh: re-read datasets and re-plot without re-building the tree.

src/PyMca5/PyMcaGui/pymca/QDispatcher.py

@@ -365,23 +365,30 @@ def _sourceSelectorSlot(self, ddict):
             if not found:
                 _logger.debug("WARNING: source not found")
                 return
-            sourceType = source.sourceType
-            del self.sourceList[self.sourceList.index(source)]
-            for source in self.sourceList:
-                if sourceType == source.sourceType:
+            closedSource = source
+            sourceType = closedSource.sourceType
+            del self.sourceList[self.sourceList.index(closedSource)]
+            try:
+                for source in self.sourceList:
+                    if sourceType == source.sourceType:
+                        self.selectorWidget[sourceType].setDataSource(source)
+                        self.tabWidget.setCurrentWidget(self.selectorWidget[sourceType])
+                        return
+                #there is no other selection of that type
+                if len(self.sourceList):
+                    source = self.sourceList[0]
+                    sourceType = source.sourceType
                     self.selectorWidget[sourceType].setDataSource(source)
-                    self.tabWidget.setCurrentWidget(self.selectorWidget[sourceType])
-                    return
-            #there is no other selection of that type
-            if len(self.sourceList):
-                source = self.sourceList[0]
-                sourceType = source.sourceType
-                self.selectorWidget[sourceType].setDataSource(source)
-            else:
-                self.selectorWidget[sourceType].setDataSource(None)
-            self.tabWidget.setCurrentWidget(self.selectorWidget[sourceType])
-        elif ddict["event"] == "SourceClosed":
-            _logger.debug("not implemented yet")
+                else:
+                    self.selectorWidget[sourceType].setDataSource(None)
+                self.tabWidget.setCurrentWidget(self.selectorWidget[sourceType])
+            finally:
+                # Without this the file stays "open" in the process
+                # and could not be reopened until PyMca restarted.
+                try:
+                    closedSource.close()
+                except Exception as e:
+                    _logger.debug("Error closing source: %s", e)
 
     def _selectionUpdatedSlot(self, ddict):
         _logger.debug("_selectionUpdatedSlot(self, dict=%s)", ddict)