RF: Separate out description generation, use column metadata if present. Fix

to icd10DescriptionFromCode

ukbparse/main.py

@@ -419,25 +419,45 @@ def doDescriptionExport(dtable, args):
         return
 
     with util.timed('Description export', log):
-        cols     = dtable.allColumns[1:]
-        vartable = dtable.vartable
+        cols = dtable.allColumns[1:]
 
         try:
             with open(args.description_file, 'wt') as f:
-                for c in cols:
-
-                    desc = vartable.loc[c.vid, 'Description']
-
-                    if desc == c.name:
-                        desc = 'n/a'
-
-                    f.write('{}\t{}\n'.format(c.name, desc))
+                for col in cols:
+                    desc = generateDescription(dtable, col)
+                    f.write('{}\t{}\n'.format(col.name, desc))
 
         except Exception as e:
             log.warning('Failed to export descriptions: {}'.format(e),
                         exc_info=True)
 
 
+def generateDescription(dtable, col):
+    """Called by :func:`doDescriptionExport`. Generates and returns a
+    suitable description for the given column.
+
+    :arg dtable: :class:`.Datatable` instance
+    :arg col:    :class:`.Column` instance
+    """
+    vartable = dtable.vartable
+    desc     = vartable.loc[col.vid, 'Description']
+
+    if desc == col.name:
+        desc = 'n/a'
+
+    # If metadata has been added to the column,
+    # we add it to the description. See the
+    # binariseCategorical processing function
+    # for an example of this.
+    if col.metadata is not None:
+        suffix = ' ({})'.format(col.metadata)
+    else:
+        suffix = ' ({}.{})'.format(col.visit, col.instance)
+
+    return '{}{}'.format(desc, suffix)
+
+
+
 def configLogging(args):
     """Configures ``ukbparse`` logging.
 

ukbparse/processing.py

@@ -367,7 +367,6 @@ def icd10DescriptionFromNumeric(val):
 @custom.metaproc('icd10.codedesc')
 def icd10DescriptionFromCode(val):
     """Generates a description for an ICD10 code. """
-    val  = icd10.codeToNumeric(val)
     hier = hierarchy.getHierarchyFilePath(name='icd10')
     hier = hierarchy.loadHierarchyFile(hier)
     desc = hier.description(val)