Add fix.py

Initial working version of metadata cleaning script that fixes lea-
ding and trailing whitespace (even in DSpace multi-value fields).

fix.py

@@ -0,0 +1,73 @@
+#!/usr/bin/env python3
+
+import pandas as pd
+
+def fix_whitespace(value):
+    """Fix whitespace issues.
+
+    Return string with leading, trailing, and consecutive whitespace trimmed.
+    """
+
+    import re
+
+    # Skip cells with missing values
+    if pd.isna(value):
+        return
+
+    # Try to split multi-value cells on "||" separator
+    #for value in cell.split('||'):
+
+    # Check for leading whitespace
+    pattern = re.compile(r'^\s+')
+    match = re.findall(pattern, value)
+
+    if len(match) > 0:
+        print('DEBUG: Leading whitespace')
+        value = re.sub(pattern, '', value)
+
+    # Check for leading whitespace in multi-value cells
+    # SOME VALUE|| ANOTHER VALUE
+    pattern = re.compile(r'\|\|\s+')
+    match = re.findall(pattern, value)
+
+    if len(match) > 0:
+        print('DEBUG: Leading whitespace in multi-value cell')
+        value = re.sub(pattern, '||', value)
+
+    # Check for trailing whitespace
+    pattern = re.compile(r'\s+$')
+    match = re.findall(pattern, value)
+
+    if len(match) > 0:
+        print('DEBUG: Trailing whitespace')
+        value = re.sub(pattern, '', value)
+
+    # Check for trailing whitespace in multi-value cells
+    # SOME VALUE ||ANOTHER VALUE
+    pattern = re.compile(r'\s+\|\|')
+    match = re.findall(pattern, value)
+
+    if len(match) > 0:
+        print('DEBUG: Trailing whitespace in multi-value cell')
+        value = re.sub(pattern, '||', value)
+
+    return value
+
+
+# Read all fields as strings so dates don't get converted from 1998 to 1998.0
+df = pd.read_csv('/home/aorth/Downloads/2019-07-26-Bioversity-Migration.csv', dtype=str)
+#df = pd.read_csv('/tmp/quality.csv')
+#df = pd.read_csv('/tmp/omg.csv')
+
+# Fix whitespace in all columns
+for column in df.columns.values.tolist():
+    print(column)
+
+    # Skip the id column
+    #if column == 'id':
+    #    continue
+
+    df[column] = df[column].apply(fix_whitespace)
+
+# Write
+df.to_csv('/tmp/omg.fixed.csv', index=False)