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Merge pull request #6 from Eh2406/overbroad_except_clauses
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replace overbroad except clauses with if statement
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@smmaurer
smmaurer authored Nov 10, 2016
2 parents 591b534 + 40f52f9 commit f156ec5
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4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -88,8 +88,8 @@ There's fairly detailed documentation of individual functions in the [source cod
| <code>max_portion_missing&nbsp;=&nbsp;portion</code> | `assert_column_max_portion_missing( table_name, column_name, portion, optional missing_val_coding )` |
| `primary_key = True` | `assert_column_is_primary_key( table_name, column_name )` |
| `foreign_key = 'parent_table_name.parent_column_name'` | <code>assert_column_is_foreign_key( table_name, column_name, parent_table_name, parent_column_name, optional&nbsp;missing_val_coding )</code> |
| `max = value` | <code>assert_column_max( table_name, column_name, max, optional&nbsp;missing_val_coding)</code> |
| `min = value` | <code>assert_column_min( table_name, column_name, min, optional&nbsp;missing_val_coding )</code> |
| `max = value` | <code>assert_column_max( table_name, column_name, maximum, optional&nbsp;missing_val_coding)</code> |
| `min = value` | <code>assert_column_min( table_name, column_name, minimum, optional&nbsp;missing_val_coding )</code> |

#### Notes

Expand Down
128 changes: 48 additions & 80 deletions orca_test/orca_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
"""


class OrcaSpec(object):

def __init__(self, name, *args):
Expand Down Expand Up @@ -60,14 +61,14 @@ class OrcaAssertionError(Exception):
__module__ = Exception.__module__



"""
#######################################
FUNCTIONS FOR WORKING WITH SPEC OBJECTS
#######################################
"""

def spec_from_yaml(str):

def spec_from_yaml(string):
return


Expand Down Expand Up @@ -148,11 +149,10 @@ def assert_column_spec(table_name, c_spec):
missing_val_coding = np.nan
for k, v in c_spec.properties.items():

if k == ('missing_val_coding'):
if k == 'missing_val_coding':
missing_val_coding = v
assert_column_missing_value_coding(table_name, c_spec.name, missing_val_coding)



# Translate the column's properties into assertion statements
for k, v in c_spec.properties.items():

Expand Down Expand Up @@ -221,20 +221,18 @@ def assert_injectable_spec(i_spec):
return



"""
###################
ASSERTION FUNCTIONS
###################
"""


def assert_table_is_registered(table_name):
"""
Has a table name been registered with orca?
"""
try:
assert orca.is_table(table_name)
except:
if not orca.is_table(table_name):
msg = "Table '%s' is not registered" % table_name
raise OrcaAssertionError(msg)
return
Expand All @@ -243,9 +241,7 @@ def assert_table_is_registered(table_name):
def assert_table_not_registered(table_name):
"""
"""
try:
assert not orca.is_table(table_name)
except:
if orca.is_table(table_name):
msg = "Table '%s' is already registered" % table_name
raise OrcaAssertionError(msg)
return
Expand All @@ -265,10 +261,11 @@ def assert_table_can_be_generated(table_name):
"""
assert_table_is_registered(table_name)

if (orca.table_type(table_name) == 'function'):
if orca.table_type(table_name) == 'function':
try:
_ = orca.get_raw_table(table_name)._call_func()
except:
# TODO: issues #3 log backtrace
msg = "Table '%s' is registered but cannot be generated" % table_name
raise OrcaAssertionError(msg)
return
Expand All @@ -292,9 +289,7 @@ def assert_column_is_registered(table_name, column_name):
assert_table_can_be_generated(table_name)
t = orca.get_table(table_name)

try:
assert (column_name in t.columns) or (column_name == t.index.name)
except:
if (column_name not in t.columns) and (column_name != t.index.name):
msg = "Column '%s' is not registered in table '%s'" % (column_name, table_name)
raise OrcaAssertionError(msg)
return
Expand All @@ -316,9 +311,7 @@ def assert_column_not_registered(table_name, column_name):
assert_table_can_be_generated(table_name)
t = orca.get_table(table_name)

try:
assert (not column_name in t.columns) and (column_name != t.index.name)
except:
if (column_name in t.columns) or (column_name == t.index.name):
msg = "Column '%s' is already registered in table '%s'" % (column_name, table_name)
raise OrcaAssertionError(msg)
return
Expand Down Expand Up @@ -347,14 +340,15 @@ def assert_column_can_be_generated(table_name, column_name):
t = orca.get_table(table_name)

# t.column_type() fails for index columns, so we have to check for them separately
if (column_name == t.index.name):
if column_name == t.index.name:
return

elif (t.column_type(column_name) == 'function'):
elif t.column_type(column_name) == 'function':
try:
# This seems to be the only way to trigger evaluation
_ = t.get_column(column_name)
except:
# TODO: issues #3 log backtrace
msg = "Column '%s' is registered but cannot be generated" % column_name
raise OrcaAssertionError(msg)
return
Expand All @@ -377,32 +371,26 @@ def assert_column_is_primary_key(table_name, column_name):
"""
assert_column_can_be_generated(table_name, column_name)

try:
idx = orca.get_table(table_name).index
assert idx.name == column_name
except:
idx = orca.get_table(table_name).index
if idx.name != column_name:
msg = "Column '%s' is not set as the index of table '%s'" \
% (column_name, table_name)
raise OrcaAssertionError(msg)

try:
assert len(idx.unique()) == len(idx)
except:
if len(idx.unique()) != len(idx):
msg = "Column '%s' is the index of table '%s' but its values are not unique" \
% (column_name, table_name)
raise OrcaAssertionError(msg)

try:
assert sum(pd.isnull(idx)) == 0
except:
if sum(pd.isnull(idx)) != 0:
msg = "Column '%s' is the index of table '%s' but it contains missing values" \
% (column_name, table_name)
raise OrcaAssertionError(msg)
return


def assert_column_is_foreign_key(table_name, column_name, parent_table_name,
parent_column_name, missing_val_coding=np.nan):
def assert_column_is_foreign_key(table_name, column_name, parent_table_name,
parent_column_name, missing_val_coding=np.nan):
"""
Asserts that a column is a foreign key whose values correspond to the primary key
column of a parent table. This confirms the integrity of "broadcast" relationships.
Expand Down Expand Up @@ -431,9 +419,7 @@ def assert_column_is_foreign_key(table_name, column_name, parent_table_name,

# Identify values in ds_child that are not in ds_parent
diff = np.setdiff1d(ds_child.values, ds_parent.values)
try:
assert len(diff) == 0
except:
if len(diff) != 0:
msg = "Column '%s.%s' has values that are not in '%s.%s'" \
% (table_name, column_name, parent_table_name, parent_column_name)
if column_name != parent_column_name:
Expand Down Expand Up @@ -462,7 +448,7 @@ def get_column_or_index(table_name, column_name):
assert_column_can_be_generated(table_name, column_name)
t = orca.get_table(table_name)

if (column_name == t.index.name):
if column_name == t.index.name:
return pd.Series(t.index)

else:
Expand All @@ -486,12 +472,10 @@ def assert_column_is_numeric(table_name, column_name):
"""
assert_column_can_be_generated(table_name, column_name)
type = get_column_or_index(table_name, column_name).dtype
dtype = get_column_or_index(table_name, column_name).dtype

try:
assert type in ['int16', 'int32', 'int64', 'float16', 'float32', 'float64']
except:
msg = "Column '%s' has type '%s' (not numeric)" % (column_name, type)
if dtype not in ['int16', 'int32', 'int64', 'float16', 'float32', 'float64']:
msg = "Column '%s' has type '%s' (not numeric)" % (column_name, dtype)
raise OrcaAssertionError(msg)
return

Expand Down Expand Up @@ -538,25 +522,22 @@ def assert_column_missing_value_coding(table_name, column_name, missing_val_codi
ds = get_column_or_index(table_name, column_name)
ds = strip_missing_values(ds, missing_val_coding)

try:
assert sum(pd.isnull(ds)) == 0
except:
if sum(pd.isnull(ds)) != 0:
msg = "Column '%s' has null entries that are not coded as %s" \
% (column_name, str(missing_val_coding))
raise OrcaAssertionError(msg)
return


def assert_column_max(table_name, column_name, max, missing_val_coding=np.nan):
def assert_column_max(table_name, column_name, maximum, missing_val_coding=np.nan):
"""
Asserts a maximum value for a numeric column, ignoring missing values.
Parameters
----------
table_name : str
column_name : str
max : int or float
Maximum value.
maximum : int or float
missing_val_coding : {0, -1, np.nan}, optional
Value that indicates missing entires.
Expand All @@ -569,25 +550,22 @@ def assert_column_max(table_name, column_name, max, missing_val_coding=np.nan):
ds = get_column_or_index(table_name, column_name)
ds = strip_missing_values(ds, missing_val_coding)

try:
assert ds.max() <= max
except:
if not ds.max() <= maximum:
msg = "Column '%s' has maximum value of %s, not %s" \
% (column_name, str(ds.max()), str(max))
% (column_name, str(ds.max()), str(maximum))
raise OrcaAssertionError(msg)
return


def assert_column_min(table_name, column_name, min, missing_val_coding=np.nan):
def assert_column_min(table_name, column_name, minimum, missing_val_coding=np.nan):
"""
Asserts a minimum value for a numeric column, ignoring missing values.
Parameters
----------
table_name : str
column_name : str
min : int or float
Minimum value.
minimum : int or float
missing_val_coding : {0, -1, np.nan}, optional
Value that indicates missing entires.
Expand All @@ -600,11 +578,9 @@ def assert_column_min(table_name, column_name, min, missing_val_coding=np.nan):
ds = get_column_or_index(table_name, column_name)
ds = strip_missing_values(ds, missing_val_coding)

try:
assert ds.min() >= min
except:
if not ds.min() >= minimum:
msg = "Column '%s' has minimum value of %s, not %s" \
% (column_name, str(ds.min()), str(min))
% (column_name, str(ds.min()), str(minimum))
raise OrcaAssertionError(msg)
return

Expand Down Expand Up @@ -636,9 +612,7 @@ def assert_column_max_portion_missing(table_name, column_name, portion, missing_
missing_pct = int(round(100 * missing_portion))
max_pct = int(round(100 * portion))

try:
assert missing_portion <= portion
except:
if not missing_portion <= portion:
msg = "Column '%s' is %s%% missing, above limit of %s%%" \
% (column_name, missing_pct, max_pct)
raise OrcaAssertionError(msg)
Expand All @@ -655,9 +629,7 @@ def assert_column_no_missing_values(table_name, column_name, missing_val_coding=
def assert_injectable_is_registered(injectable_name):
"""
"""
try:
assert orca.is_injectable(injectable_name)
except:
if not orca.is_injectable(injectable_name):
msg = "Injectable '%s' is not registered" % injectable_name
raise OrcaAssertionError(msg)
return
Expand All @@ -666,9 +638,7 @@ def assert_injectable_is_registered(injectable_name):
def assert_injectable_not_registered(injectable_name):
"""
"""
try:
assert not orca.is_injectable(injectable_name)
except:
if orca.is_injectable(injectable_name):
msg = "Injectable '%s' is already registered" % injectable_name
raise OrcaAssertionError(msg)
return
Expand All @@ -692,10 +662,11 @@ def assert_injectable_can_be_generated(injectable_name):
"""
assert_injectable_is_registered(injectable_name)

if (orca.injectable_type(injectable_name) == 'function'):
if orca.injectable_type(injectable_name) == 'function':
try:
_ = orca.get_injectable(injectable_name)
except:
# TODO: issues #3 log backtrace
msg = "Injectable '%s' is registered but cannot be evaluated" % injectable_name
raise OrcaAssertionError(msg)
return
Expand All @@ -714,32 +685,32 @@ def assert_injectable_is_numeric(injectable_name):
return


def assert_injectable_greater_than(injectable_name, min):
def assert_injectable_greater_than(injectable_name, minimum):
"""
Asserts that a numeric injectable is greater than or equal to a minimum value.
"""
assert_injectable_is_numeric
assert_injectable_is_numeric(injectable_name)
inj = orca.get_injectable(injectable_name)

if not inj >= min:
if not inj >= minimum:
msg = "Injectable '%s' has value of %s, less than %s" \
% (injectable_name, str(inj), str(min))
% (injectable_name, str(inj), str(minimum))
raise OrcaAssertionError(msg)
return


def assert_injectable_less_than(injectable_name, max):
def assert_injectable_less_than(injectable_name, maximum):
"""
Asserts that a numeric injectable is less than or equal to a maximum value.
"""
assert_injectable_is_numeric
assert_injectable_is_numeric(injectable_name)
inj = orca.get_injectable(injectable_name)

if not inj <= max:
if not inj <= maximum:
msg = "Injectable '%s' has value of %s, greater than %s" \
% (injectable_name, str(inj), str(max))
% (injectable_name, str(inj), str(maximum))
raise OrcaAssertionError(msg)
return

Expand All @@ -758,6 +729,3 @@ def assert_injectable_has_key(injectable_name, key):
msg = "Injectable '%s' does not have key '%s'" % (injectable_name, key)
raise OrcaAssertionError(msg)
return



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