Bug fix to enable quality flags to be identified as level data. Inclu…

…de tests in testing module for Temperature_IQUODflags.

tests/netcdf_test.py

@@ -23,7 +23,7 @@ def test_longitude(classic1):
     '''
 
     longitude = classic1.longitude()
-    assert round(longitude, 2) == -172.270, 'longitude should have been approx -172.270, instead read %f' % latitude
+    assert round(longitude, 2) == -172.270, 'longitude should have been approx -172.270, instead read %f' % longitude
 
 def test_uid(classic1):
     '''
@@ -110,6 +110,34 @@ def test_temperature(classic1):
     t = classic1.t()
     assert numpy.array_equal(t, truth), 'temperatures should have been [8.96, 8.95, 0.9, -1.23], instead read %s' % t.__str__()
 
+def test_temperature_WODflags(classic1):
+    '''
+    check WOD flags are not returned = [--, --, --, --]
+    '''
+
+    qc = classic1.t_level_qc('WOD')
+    assert numpy.alltrue(qc.mask) , \
+        'temperature_WODflags should not be in file, instead read %s' % qc.__str__()
+
+
+def test_temperature_IQUODflags(classic1):
+    '''
+    check IQUOD flags are returned = [0, 0, 0, 0]
+    '''
+
+    errors = []
+    truth = [0, 0, 0, 0]
+    qc = classic1.t_level_qc('IQUOD')
+    # replace assertions by conditions
+    if numpy.alltrue(qc.mask):
+        errors.append("Temperature_IQUODflags not found in file")
+    if not numpy.array_equal(qc, truth):
+        errors.append('Temperature_IQUODflags should have been [0, 0, 0, 0], instead read %s' % qc.__str__())
+
+    # assert no error message has been registered, else print messages
+    assert not errors, "errors occured:\n{}".format("\n".join(errors))
+
+
 def test_salinity(classic1):
     '''
     check salinities == [30.900, 30.900, 31.910, 32.410]

wodpy/wodnc.py

@@ -36,7 +36,12 @@ def __init__(self, filename):
         '''
         filename: name of netcdf file containing wod profiles
         '''
-        self.rootgrp = Dataset(filename, "r", format="NETCDF4")
+        if isinstance(filename, str):
+            self.rootgrp = Dataset(filename, "r", format="NETCDF4")
+        else:
+            # if this is a file object from s3 bucket
+            nc_bytes = filename.read()
+            self.rootgrp = Dataset(f'inmemory.nc', 'r', format='NETCDF4', memory=nc_bytes)
 
     def ncasts(self):
         return self.rootgrp.dimensions['casts'].size
@@ -97,6 +102,8 @@ def locate_in_ragged(self, v):
         '''
         returns (offset, nentries) for variable v to extract it for this profile from the raggedarray.
         '''
+        # trim variable v to ust include the variable name left of any underscore:
+        v = v.split('_')[0]
         offset = self.determine_offset(v+'_row_size')
         nentries = self.metadata(v+'_row_size')
         return offset, nentries
@@ -127,11 +134,16 @@ def is_level_data(self, data_key):
         returns true if data_key looks like per level data
         '''
 
-        if data_key + '_obs' in self.r.dimensions():
+        if data_key not in self.r.rootgrp.variables.keys():
+            return False
+        if len(self.r.rootgrp.variables[data_key].dimensions) == 0:
+            logging.warning(data_key + ' not level data.')
+            return False
+        if '_obs' in self.r.rootgrp.variables[data_key].dimensions[0]:
             # per level data should have a *_obs dimension 
             return True
         else:
-            logging.warning(data_key + ' not found in this dataset.')
+            logging.warning(data_key + ' not level data.')
             return False                    
 
     def show_profile_metadata(self):