app.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

from flask import Flask, render_template, make_response
from model import app, db, WorkTime, Employee, Project
import csv



def create_csv():
    with open('/tmp/worktime.csv', 'w') as f:
        rows = db.session.query(WorkTime, Employee, Project) \
            .filter(WorkTime.employee_id==Employee.id) \
            .filter(WorkTime.project_id==Project.id).all()
        csvwriter = csv.writer(f)
        csvwriter.writerows([(w.date, e.name, p.name, w.kind, w.ratio) for w, e, p in rows])

@app.route('/download')
def download():
#    create_csv() ここのコメントアウト外すと例外が飛ぶ
    return make_response('TO BE IMPLEMENTED')

@app.route('/')
def index():
    return render_template('index.html')


if __name__ == '__main__':
    app.debug = True
    app.run()

model.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

from flask import Flask
from flaskext.sqlalchemy import SQLAlchemy

app = Flask(__name__)
# url = 'mysql://worktime:[email protected]/worktime'
url = 'mysql://kinebuchi@localhost/test'
app.config['SQLALCHEMY_DATABASE_URI'] = url
db = SQLAlchemy(app)


class Employee(db.Model):
    id = db.Column(db.Integer, primary_key=True)
    code = db.Column(db.String(45))
    name = db.Column(db.String(45))
    worktimes = db.relation('WorkTime', backref='employee')

    def __init__(self, code, name):
        self.code = code
        self.name = name

    def __repr(self):
        return '<Employee {0}, {1}, {2}>'.format(self.id, self.code, self.name)

class Project(db.Model):
    id = db.Column(db.Integer, primary_key=True)
    code = db.Column(db.String(20))
    name = db.Column(db.String(20))
    status = db.Column(db.Enum('PLANNED', 'RUNNING', 'FINISHED'),
                       default='PLANNED')
    worktimes = db.relation('WorkTime', backref='project')

    def __init__(self, code, name, status='PLANNED'):
        self.code = code
        self.name = name
        self.status = status

    def __repr__(self):
        return '<Project {0}, {1}, {2}, {3}>'.format(self.id, self.code,
                                                     self.name, self.status)

class WorkTime(db.Model):
    date = db.Column(db.Date, primary_key=True)
    employee_id = db.Column(db.Integer, db.ForeignKey('employee.id'),
                              primary_key=True)
    project_id = db.Column(db.Integer, db.ForeignKey('project.id'),
                             primary_key=True)
    kind = db.Column(db.Enum('BUDGET', 'ACTUAL'), primary_key=True)
    ratio = db.Column(db.Float, default=0)

    def __init__(self, date, employee_id, project_id, kind, ratio):
        self.date = date
        self.employee_id = employee_id
        self.project_id = project_id
        self.kind = kind
        self.ratio = ratio

    def __repr__(self):
        return '<WorkTime {0}, {1}, {2}, {3}, {4}>'.format(self.date,
                                                           self.employee_id,
                                                           self.project_id,
                                                           self.kind,
                                                           self.ratio)

git clone して以下の変更を加えたところ、例外は発生しませんでした。
(db.create_all() は手動で行いました)

diff --git a/app.py b/app.py
index 8c6c040..4161bf3 100644
--- a/app.py
+++ b/app.py
@@ -17,7 +17,7 @@ def create_csv():

@app.route('/download')
def download():
-# create_csv() ここのコメントアウト外すと例外が飛ぶ

• create_csv()
  return make_response('TO BE IMPLEMENTED')

@app.route('/')
diff --git a/model.py b/model.py
index 584039f..5263b7a 100644
--- a/model.py
+++ b/model.py
@@ -6,7 +6,8 @@ from flaskext.sqlalchemy import SQLAlchemy

app = Flask(name)

url = 'mysql://worktime:[email protected]/worktime'

-url = 'mysql://kinebuchi@localhost/test'
+#url = 'mysql://kinebuchi@localhost/test'
+url = 'sqlite:///test.db'
app.config['SQLALCHEMY_DATABASE_URI'] = url
db = SQLAlchemy(app)