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Change printed errors to raised exceptions #72

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merged 2 commits into from
Feb 20, 2018
Merged

Change printed errors to raised exceptions #72

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2c2e863
Raise exception during error instead of printing error message
philerooski Feb 20, 2018
2e9c5bf
pep8
philerooski Feb 20, 2018
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58 changes: 26 additions & 32 deletions annotator/Pipeline.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,29 +79,28 @@ def undo(self):
self._activeCols = backup._activeCols
print("Undo: {}".format(message))
else:
print("At last available change.")
raise IndexError("At last available change.")

def head(self):
""" Print head of `self.view` """
if hasattr(self.view, 'head'):
print(self.view.head())
else:
print("No data view set.")
raise AttributeError("No data view set.")

def tail(self):
""" Print tail of `self.view` """
if hasattr(self.view, 'tail'):
print(self.view.tail())
else:
print("No data view set")
raise AttributeError("No data view set.")

def shape(self):
""" Print shape of `self.view` """
if hasattr(self.view, 'shape'):
print(self.view.shape)
else:
print("No data view set.")

raise AttributeError("No data view set.")

def drop(self, labels, axis):
""" Delete rows or columns from a file view on Synapse.*
Expand Down Expand Up @@ -133,27 +132,26 @@ def drop(self, labels, axis):
for l in self.schema.key]]
self.view = self.view.drop(labels, axis=axis)


def metaHead(self):
""" Print head of `self._meta` """
if hasattr(self._meta, 'head'):
print(self._meta.head())
else:
print("No metadata view set.")
raise AttributeError("No metadata view set.")

def metaTail(self):
""" Print tail of `self._meta` """
if hasattr(self._meta, 'tail'):
print(self._meta.tail())
else:
print("No metadata view set.")
raise AttributeError("No metadata view set.")

def metaShape(self):
""" Print shape of `self._meta` """
if hasattr(self._meta, 'shape'):
print(self._meta.shape)
else:
print("No metadata view set.")
raise AttributeError("No metadata view set.")

def columns(self, style="numbers"):
""" Pretty print `self.view.columns`.
Expand All @@ -166,7 +164,7 @@ def columns(self, style="numbers"):
if hasattr(self.view, 'columns'):
self._prettyPrintColumns(self.view.columns, style)
else:
print("No data view set.")
raise AttributeError("No data view set.")

def metaColumns(self, style="numbers"):
""" Pretty print `self._meta.columns`.
Expand All @@ -179,7 +177,7 @@ def metaColumns(self, style="numbers"):
if hasattr(self._meta, 'columns'):
self._prettyPrintColumns(self._meta.columns, style)
else:
print("No metadata view set.")
raise AttributeError("No metadata view set.")

def activeColumns(self, style="numbers"):
""" Pretty print `self._activeCols`.
Expand Down Expand Up @@ -207,7 +205,6 @@ def metaActiveColumns(self, style="numbers"):
else:
print("No active columns.")


def addView(self, scope):
""" Add further Folders/Projects to the scope of `self.view`.

Expand All @@ -229,19 +226,19 @@ def addView(self, scope):
raise RuntimeError("Must first create a file view if the "
"view is not yet set and not all items in "
"the scope are File Views or Schemas.")
self._entityViewSchema = utils.addToScope(self.syn,
self._entityViewSchema, scope)
self._entityViewSchema = utils.addToScope(
self.syn, self._entityViewSchema, scope)
# Assuming row version/id values stay the same for the before-update
# rows, we can carry over values from the old view.
oldIndices = self._index
oldColumns = self.view.columns
newView = utils.synread(self.syn, self._entityViewSchema.id, silent=True)
newView = utils.synread(
self.syn, self._entityViewSchema.id, silent=True)
for c in oldColumns:
newView.loc[oldIndices,c] = self.view[c].values
newView.loc[oldIndices, c] = self.view[c].values
self.view = newView
self._index = self.view.index


def addActiveCols(self, activeCols, path=False, isMeta=False, backup=True):
""" Add column names to `self._activeCols` or `self._metaActiveCols`.

Expand Down Expand Up @@ -295,8 +292,7 @@ def addDefaultValues(self, colVals, backup=True):
column values. Defaults to True.
"""
if self.view is None:
print("No data view set.")
return
raise AttributeError("No data view set.")
if backup:
self.backup("addDefaultValues")
for k in colVals:
Expand All @@ -305,17 +301,16 @@ def addDefaultValues(self, colVals, backup=True):
def addKeyCol(self):
""" Add a key column to `self.view`.

A key column is a column in `self.view` whose values can be matched in a
one-to-one manner with the column values of a column in `self._meta`.
A key column is a column in `self.view` whose values can be matched in
a one-to-one manner with the column values of a column in `self._meta`.
Usually this involves applying a regular expression to one of the
columns in `self.view`. After a regular expression which satisfies the
users requirements is found, the key column is automatically added to
`self.view` with the same name as the column matched upon
in `self._meta`.
"""
if self.view is None or self._meta is None:
print("No data view set.")
return
raise AttributeError("No data view set.")
self.backup("addKeyCol")
link = self._linkCols(1)
dataKey, metaKey = link.popitem()
Expand Down Expand Up @@ -401,8 +396,7 @@ def addLinks(self, links=None, append=True, backup=True):
Links stored in `self.links`.
"""
if self.view is None or self._meta is None:
print("No data view set.")
return
raise AttributeError("No data view set.")
if backup:
self.backup("addLinks")
if links is None:
Expand Down Expand Up @@ -564,11 +558,12 @@ def _validate(self):
malformed_values = schemaModule.validateView(self.view, self.schema)
if malformed_values:
for k in malformed_values:
warnings.append("{} contains the following values which are "
"not specified in the schema: {}".format(
k, ", ".join(map(str, malformed_values[k]))) +
"\n\tPossible values are {}".format(
", ".join(self.schema.loc[k].value.values)))
warnings.append(
"{} contains the following values which are "
"not specified in the schema: {}".format(
k, ", ".join(map(str, malformed_values[k]))) +
"\n\tPossible values are {}".format(
", ".join(self.schema.loc[k].value.values)))
return warnings

def removeActiveCols(self, activeCols):
Expand Down Expand Up @@ -789,8 +784,7 @@ def inferValues(self, col, referenceCols):
Column(s) to match on.
"""
if self.view is None:
print("No data view set.")
return
raise AttributeError("No data view set.")
self.backup("inferValues")
self.view = utils.inferValues(self.view, col, referenceCols)

Expand Down
2 changes: 1 addition & 1 deletion annotator/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -329,7 +329,7 @@ def inferValues(df, col, referenceCols):
df.loc[df[referenceCols] == k, col] = v[0]
else:
print("Unable to infer value when {} = {}".format(
referenceCols, k))
referenceCols, k))
return df


Expand Down