Refactor as package with subpackages

This makes it cleaner for introducing checks, fixes, tests, docs,
and tests in the future. Currently can be run like this:

  python -m csv_metadata_quality

CSV input and output paths are still hard coded.

See: https://dev.to/codemouse92/dead-simple-python-project-structure-and-imports-38c6

csv_metadata_quality/__main__.py

@@ -0,0 +1,4 @@
+from csv_metadata_quality import app
+
+if __name__ == '__main__':
+        app.run()

csv_metadata_quality/app.py

@@ -0,0 +1,17 @@
+import csv_metadata_quality.fix as fix
+import pandas as pd
+
+def run():
+    # 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', dtype=str)
+    df = pd.read_csv('/tmp/omg.csv', dtype=str)
+
+    # Fix whitespace in all columns
+    for column in df.columns.values.tolist():
+        print(f'DEBUG: {column}')
+
+        df[column] = df[column].apply(fix.whitespace)
+
+    # Write
+    df.to_csv('/tmp/omg.fixed.csv', index=False)

csv_metadata_quality/fix.py

@@ -0,0 +1,42 @@
+import pandas as pd
+import re
+
+def alan():
+    print('Alan')
+
+
+def whitespace(field):
+    """Fix whitespace issues.
+
+    Return string with leading, trailing, and consecutive whitespace trimmed.
+    """
+
+
+    # Skip fields with missing values
+    if pd.isna(field):
+        return
+
+    # Initialize an empty list to hold the cleaned values
+    values = list()
+
+    # Try to split multi-value field on "||" separator
+    for value in field.split('||'):
+        # Strip leading and trailing whitespace
+        value = value.strip()
+
+        # Replace excessive whitespace (>2) with one space
+        pattern = re.compile(r'\s{2,}')
+        match = re.findall(pattern, value)
+
+        if len(match) > 0:
+            print('DEBUG: Excessive whitespace')
+            value = re.sub(pattern, ' ', value)
+
+        # Save cleaned value
+        values.append(value)
+
+    # Create a new field consisting of all values joined with "||"
+    new_field = '||'.join(values)
+
+    return new_field
+