Open database connection with 'w' instead of 'r' for writing

Summary:
there are several places we open an 'r' connection but use it
for writing. Fix them.

Test Plan:
ran parse_one_commit.php against one revision which executes
the code with problem. It used to throw exception. Now it works fine.

Reviewed By: Girish
Reviewers: tuomaspelkonen, Girish
Commenters: aran
CC: aran, Girish
Differential Revision: 213