From a20d7738b61ab4cf7f7b153b60768c404c68386f Mon Sep 17 00:00:00 2001
From: Ramkrishna Chakrabarty <rc@bx.psu.edu>
Date: Tue, 8 Mar 2011 12:42:26 -0500
Subject: [PATCH] Fixes the data corruption caused in the form_values table
 (content field) by the migrate script 65.

---
 .../0076_fix_form_values_data_corruption.py   | 78 +++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py

diff --git a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
new file mode 100644
index 00000000000..255bc2c5ef4
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
@@ -0,0 +1,78 @@
+'''
+This migration script fixes the data corruption caused in the form_values
+table (content json field) by migrate script 65.
+'''
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+from sqlalchemy.exc import *
+
+from galaxy.util.json import from_json_string, to_json_string
+from galaxy.model.custom_types import _sniffnfix_pg9_hex
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    
+    cmd = "SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fields " \
+          + " FROM form_definition, form_values " \
+          + " WHERE form_values.form_definition_id=form_definition.id " \
+          + " ORDER BY form_values.id"
+    result = db_session.execute( cmd )
+    corrupted_rows = 0
+    for row in result:
+        # first check if loading the dict from the json succeeds
+        # if that fails, it means that the content field is corrupted.
+        try:
+            field_values_dict = from_json_string( str( row['field_values'] ) )
+        except Exception, e:
+            corrupted_rows = corrupted_rows + 1
+            # content field is corrupted
+            fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fields'] ) ) )
+            field_values_str = _sniffnfix_pg9_hex( str( row['field_values'] ) )
+            field_values_dict = {}
+            # look for each field name in the values and extract its value (string)
+            for index in range( len(fields_list) ):
+                field = fields_list[index]
+                field_name_key = '"%s": "' % field['name']
+                field_index = field_values_str.find( field_name_key )
+                if field_index == -1:
+                    # if the field name is not present the field values dict then 
+                    # inform the admin that this form values cannot be fixed 
+                    print "The 'content' field of row 'id' %i does not have the field '%s' in the 'form_values' table and could not be fixed by this migration script." % ( int( field['id'] ), field['name'] )
+                else:
+                    # check if this is the last field
+                    if index == len( fields_list )-1:
+                        # since this is the last field, the value string lies between the
+                        # field name and the '"}' string at the end, hence len(field_values_str)-2
+                        value = field_values_str[ field_index+len( field_name_key ):len( field_values_str )-2 ]
+                    else:
+                        # if this is not the last field then the value string lies between
+                        # this field name and the next field name
+                        next_field = fields_list[index+1]
+                        next_field_index = field_values_str.find( '", "%s": "' % next_field['name'] )
+                        value = field_values_str[ field_index+len( field_name_key ):next_field_index ]
+                    # clean up the value string, escape the required quoutes and newline characters
+                    value = value.replace( "'", "\''" )\
+                                 .replace( '"', '\\\\"' )\
+                                 .replace( '\r', "\\\\r" )\
+                                 .replace( '\n', "\\\\n" )\
+                                 .replace( '\t', "\\\\t" )
+                    # add to the new values dict
+                    field_values_dict[ field['name'] ] = value
+            # update the db
+            json_values = to_json_string(field_values_dict)
+            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( json_values, int( row['id'] ) )
+            db_session.execute( cmd )
+    print 'Fixed %i corrupted rows.' % corrupted_rows
+
+def downgrade():
+    pass
\ No newline at end of file