Use a cascading search to determine the time dimension (#145)

* Use a cascading search to determine the time dimension

The assumption that time was the only record dimension in a file was
not particularly robust against real data. We instead check:
- standard_name == 'time'
- axis == 'T'
- record dimension
- name.lower() == 'time'

Fixes #144.

* Check dimension in dataset variables

A dimension without an associated variable causes a KeyError when
we're looking for dimensions that contain a particular attribute, when
this should just count as not finding the attribute.

cosima_cookbook/database.py

@@ -172,7 +172,7 @@ def update_timeinfo(f, ncfile):
 
     with netCDF4.Dataset(f, 'r') as ds:
         # we assume the record dimension corresponds to time
-        time_dim = netcdf_utils.find_record_dimension(ds)
+        time_dim = netcdf_utils.find_time_dimension(ds)
         if time_dim is None:
             return None
 

cosima_cookbook/netcdf_utils.py

@@ -6,3 +6,42 @@ def find_record_dimension(d):
             return dim
 
     return None
+
+def find_dimension_with_attribute(d, attribute, value):
+    """Find a matching dimension with attribute=value, or None."""
+
+    for dim in d.dimensions:
+        if dim not in d.variables:
+            continue
+
+        if getattr(d.variables[dim], attribute, None) == value:
+            return dim
+
+    return None
+
+def find_time_dimension(d):
+    """Find a time dimension in a netCDF4 Dataset."""
+
+    # this is a bit heuristic, but we cascade through some checks, guided by
+    # the CF conventions
+
+    dim = find_dimension_with_attribute(d, 'standard_name', 'time')
+    if dim is not None:
+        return dim
+
+    dim = find_dimension_with_attribute(d, 'axis', 'T')
+    if dim is not None:
+        return dim
+
+    dim = find_record_dimension(d)
+    if dim is not None:
+        return dim
+
+    for dim in d.dimensions:
+        if dim.lower() == 'time':
+            return dim
+
+    # CF conventions also suggests the units attribute,
+    # but time_bounds may have the same units, and a false positive
+    # here could be very confusing...
+    return None

test/test_indexing.py

@@ -170,6 +170,16 @@ def test_broken_metadata(session_db):
 
     assert(indexed == 1)
 
+def test_time_dimension(session_db):
+    session, db = session_db
+    database.build_index('test/data/indexing/time', session)
+
+    q = session.query(database.NCFile.time_start, database.NCFile.time_end)
+    assert(q.count() == 4) # should pick up 4 files
+
+    q = q.filter((database.NCFile.time_start is None) | (database.NCFile.time_end is None))
+    assert(q.count() == 0) # but all of them should have times populated
+
 def test_distributed(client, session_db):
     session, db = session_db
     database.build_index('test/data/indexing/broken_file', session, client)