refact(table): encapsulate buf.getCell() & improve logging

+ Centralize error-reporting for cell indexing-errors.
+ Logging:
  + Restore start offset-logging on cell indexing errors.
  + Class-logger-->module-var, not to waste loggers with each new
object.
  + Stop specifying log-levels (must be done to all loggers).

vitables/plugins/timeseries/time_series.py

@@ -231,7 +231,7 @@ def customiseModel(self, datasheet):
             leaf_kind = 'array'
         model_info = {
             'leaf_kind': leaf_kind,
-            'rbuffer': model.rbuffer,
+            'model': model,
             'numrows': model.rowCount(),
             'formatContent': model.formatContent,
         }
@@ -298,7 +298,7 @@ def __init__(self, model_info, ts_info, parent=None):
         self.ts_freq = ts_info['ts_freq']
         self.ts_format = ts_info['ts_format']
         # Attributes required by the data() method
-        self.rbuffer = model_info['rbuffer']
+        self.model = model_info['model']
         self.numrows = model_info['numrows']
         self.ts_cols = ts_info['ts_cols']
         self.formatContent = model_info['formatContent']
@@ -322,12 +322,13 @@ def table_data(self, index, role=QtCore.Qt.DisplayRole):
         - `index`: the index of a data item
         - `role`: the role being returned
         """
+        row, col = index.row(), index.column()
 
-        if not index.isValid() or not (0 <= index.row() < self.nrows):
+        if not index.isValid() or not (0 <= row < self.nrows):
             return None
 
         if role == QtCore.Qt.DisplayRole:
-            cell = self.rbuffer.getCell(index.row(), index.column())
+            cell = self.model.cell(row, col)
             if index.column() in self.ts_cols:
                 return self.tsFormatter(cell)
             return self.formatContent(cell)
@@ -348,12 +349,13 @@ def array_data(self, index, role=QtCore.Qt.DisplayRole):
         - `index`: the index of a data item
         - `role`: the role being returned
         """
+        row, col = index.row(), index.column()
 
-        if not index.isValid() or not (0 <= index.row() < self.nrows):
+        if not index.isValid() or not (0 <= row < self.nrows):
             return None
 
         if role == QtCore.Qt.DisplayRole:
-            cell = self.rbuffer.getCell(index.row(), index.column())
+            cell = self.model.cell(row, col)
             return self.tsFormatter(cell)
 
         if role == QtCore.Qt.TextAlignmentRole:

vitables/vttables/buffer.py

@@ -48,6 +48,8 @@
 warnings.filterwarnings('ignore', category=tables.FlavorWarning)
 warnings.filterwarnings('ignore', category=tables.NaturalNameWarning)
 
+log = logging.getLogger(__name__)
+
 
 class Buffer(object):
     """Buffer used to access the real data contained in `PyTables` datasets.
@@ -81,9 +83,6 @@ def __init__(self, leaf):
         Initializes the buffer.
         """
 
-        self.logger = logging.getLogger(__name__)
-        self.logger.setLevel(logging.INFO)
-
         self.leaf = leaf
 
         # The numpy array where read data will be stored
@@ -161,7 +160,7 @@ def isDataSourceReadable(self):
         except tables.HDF5ExtError:
             readable = False
             # TODO: Fix error msg to include exception or merge with below.
-            self.logger.error(
+            log.error(
                 translate('Buffer',
                           """Problems reading records. The dataset """
                           """seems to be compressed with the {0} library. """
@@ -171,7 +170,7 @@ def isDataSourceReadable(self):
                               self.leaf.filters.complib))
         except ValueError as e:
             readable = False
-            self.logger.error(
+            log.error(
                 translate('Buffer', 'Data read error: {}',
                           'A dataset read error').format(e.message))
         return readable
@@ -204,7 +203,7 @@ def readBuffer(self, start, stop):
             data = self.leaf.read(start, stop)
         except tables.HDF5ExtError:
             # TODO: Fix error msg to include exception.
-            self.logger.error(
+            log.error(
                 translate('Buffer', """\nError: problems reading records. """
                           """The dataset maybe corrupted.""",
                           'A dataset readability error'))
@@ -228,12 +227,7 @@ def scalarCell(self, row, col):
 
         :Returns: the cell at position `(row, col)` of the document
         """
-
-        try:
-            return self.chunk[()]
-        except IndexError:
-            self.logger.error('IndexError! row, column: {1}, {2}'
-                              .format(row, col))
+        return self.chunk[()]
 
     def vectorCell(self, row, col):
         """
@@ -260,11 +254,7 @@ def vectorCell(self, row, col):
         # get the right chunk element.
         # chunk = [row0, row1, row2, ..., rowN]
         # and columns can be read from a given row using indexing notation
-        try:
-            return self.chunk[row]
-        except IndexError:
-            self.logger.error('IndexError! row, column: {1}, {2}'
-                              .format(row, col))
+        return self.chunk[row]
 
     def EArrayCell(self, row, col):
         """
@@ -287,11 +277,7 @@ def EArrayCell(self, row, col):
         # and columns can be read from a given row using indexing notation
         # TODO: this method should be improved as it requires to read the
         # whola array keeping the read data in memory
-        try:
-            return self.leaf.read()[row]
-        except IndexError:
-            self.logger.error('IndexError! row, column: {1}, {2}'
-                              .format(row, col))
+        return self.leaf.read()[row]
 
     def arrayCell(self, row, col):
         """
@@ -316,8 +302,4 @@ def arrayCell(self, row, col):
         # For tables we have
         # chunk = [nestedrecord0, nestedrecord1, ..., nestedrecordN]
         # and fields can be read from nestedrecordJ using indexing notation
-        try:
-            return self.chunk[row][col]
-        except IndexError:
-            self.logger.error('IndexError! row, column: {1}, {2}'
-                              .format(row, col))
+        return self.chunk[row][col]

vitables/vttables/datasheet.py

@@ -94,7 +94,6 @@ def __init__(self, index):
         self.aboutToActivate.connect(self.syncTreeView)
         self.leaf_view.doubleClicked.connect(self.zoomCell)
 
-
     def closeEvent(self, event):
         """Close the window cleanly with the close button of the title bar.
 
@@ -112,7 +111,6 @@ def closeEvent(self, event):
         if self.vtgui.workspace.subWindowList() == []:
             self.vtgui.dbs_tree_view.setFocus(True)
 
-
     def focusInEvent(self, event):
         """Specialised handler for focus events.
 
@@ -128,7 +126,6 @@ def focusInEvent(self, event):
         self.syncTreeView()
         self.setFocus(True)
 
-
     def syncTreeView(self):
         """
         If the view is activated select its leaf in the tree of databases view.
@@ -143,7 +140,6 @@ def syncTreeView(self):
         self.vtgui.dbs_tree_view.setCurrentIndex(
             QtCore.QModelIndex(self.pindex))
 
-
     def zoomCell(self, index):
         """Display the inner dimensions of a cell.
 
@@ -153,18 +149,18 @@ def zoomCell(self, index):
         row = index.row()
         column = index.column()
         tmodel = index.model()
-        data = tmodel.rbuffer.getCell(row, column)
+        data = tmodel.cell(row, column)
 
         # The title of the zoomed view
         node = self.dbt_leaf
         info = nodeinfo.NodeInfo(node)
         if node.node_kind == 'table':
             col = info.columns_names[column]
             title = '{0}: {1}[{2}]'.format(node.name, col,
-                tmodel.start + row)
+                                           tmodel.start + row)
         else:
             title = '{0}: ({1},{2})'.format(node.name,
-                tmodel.start + row, column)
+                                            tmodel.start + row, column)
 
         zoom_cell.ZoomCell(data, title, self.vtgui.workspace,
-                          self.dbt_leaf)
+                           self.dbt_leaf)

vitables/vttables/leaf_model.py

@@ -26,17 +26,19 @@
 
 __docformat__ = 'restructuredtext'
 
+import logging
 import vitables.utils
+from vitables.vttables import buffer
 
 from qtpy import QtCore
 import tables
 
-from vitables.vttables import buffer
-
 
 #: The maximum number of rows to be read from the data source.
 CHUNK_SIZE = 10000
 
+log = logging.getLogger(__name__)
+
 
 class LeafModel(QtCore.QAbstractTableModel):
     """
@@ -207,15 +209,23 @@ def data(self, index, role=QtCore.Qt.DisplayRole):
         - `index`: the index of a data item
         - `role`: the role being returned
         """
+        row, col = index.row(), index.column()
 
-        if not index.isValid() or not (0 <= index.row() < self.numrows):
+        if not index.isValid() or not (0 <= row < self.numrows):
             return None
 
         if role == QtCore.Qt.DisplayRole:
-            cell = self.rbuffer.getCell(index.row(), index.column())
+            cell = self.cell(row, col)
             return self.formatContent(cell)
 
         if role == QtCore.Qt.TextAlignmentRole:
             return QtCore.Qt.AlignLeft | QtCore.Qt.AlignTop
 
         return None
+
+    def cell(self, row, col):
+        try:
+            return self.rbuffer.getCell(row, col)
+        except IndexError:
+            log.error('IndexError! buffer start: {0} row, column: '
+                      '{1}, {2}'.format(self.start, row, col))