app: Fix bug with wrong PRIMARY KEY

Having PRIMARY KEY on certificate.id is to strict -- as real uniques is
required on id + reference in certificate table.

kedifa/app.py

@@ -80,12 +80,13 @@ class SQLite3Storage(local):
           active INTEGER
         );
         CREATE TABLE IF NOT EXISTS certificate (
-          id INTEGER PRIMARY KEY,
+          id INTEGER,
           reference VARCHAR(255),
           submission_date INTEGER,
           not_valid_before_date INTEGER,
           not_valid_after_date INTEGER,
-          pem TEXT
+          pem TEXT,
+          PRIMARY KEY (id, reference)
         );
         CREATE TABLE IF NOT EXISTS counter (
           name TEXT PRIMARY KEY,

kedifa/test.py

@@ -714,9 +714,11 @@ class KedifaIntegrationTest(unittest.TestCase):
       result.text
     )
 
-  def generateauth(self):
+  def generateauth(self, reference=None):
+    if reference is None:
+      reference = self.reference
     result = self.requests_get(
-      self.kedifa_url + self.reference + '/generateauth')
+      self.kedifa_url + reference + '/generateauth')
     self.assertEqual(
       httplib.CREATED,
       result.status_code
@@ -779,6 +781,28 @@ class KedifaIntegrationTest(unittest.TestCase):
   def test_PUT(self):
     self.put()
 
+  def test_PUT_multiple_same_reference(self):
+    auth = self.generateauth()
+    self.put(auth=auth)
+    _, key_pem, _, certificate_pem = self.generateKeyCertificateData(
+      not_valid_before=datetime.datetime.utcnow() - datetime.timedelta(days=4),
+      not_valid_after=datetime.datetime.utcnow() + datetime.timedelta(days=2)
+    )
+    self.put(data=key_pem + certificate_pem, auth=auth)
+
+  def test_PUT_multiple_different_reference(self):
+    # put first certificate
+    self.put()
+
+    # put another certificate on another reference
+    reference = self.reserveReference()
+    auth = self.generateauth(reference)
+    _, key_pem, _, certificate_pem = self.generateKeyCertificateData(
+      not_valid_before=datetime.datetime.utcnow() - datetime.timedelta(days=4),
+      not_valid_after=datetime.datetime.utcnow() + datetime.timedelta(days=2)
+    )
+    self.put(key=reference, data=key_pem + certificate_pem, auth=auth)
+
   def test_PUT_certificate_expired(self):
     _, key_pem, _, certificate_pem = self.generateKeyCertificateData(
       not_valid_before=datetime.datetime.utcnow() - datetime.timedelta(days=4),