Merge branch 'master' into nomenclature

Conflicts:
	test/data/test.db

data/migrations/env.py

@@ -5,7 +5,7 @@ import os
 from alembic import context
 from sqlalchemy import engine_from_config, pool
 from logging.config import fileConfig
-from urllib import unquote
+from urllib import unquote, quote
 from peewee import SqliteDatabase
 
 from data.database import all_models, db
@@ -24,6 +24,11 @@ if 'GENMIGRATE' in os.environ:
     else:
         db_uri = 'postgresql://postgres@%s/genschema' % (docker_host_ip)
 
+if 'DB_URI' in os.environ:
+    db_uri = os.environ['DB_URI']
+
+app.config['DB_URI'] = db_uri
+
 config = context.config
 config.set_main_option('sqlalchemy.url', db_uri)
 
@@ -69,7 +74,7 @@ def run_migrations_online():
 
     """
 
-    if isinstance(db.obj, SqliteDatabase) and not 'GENMIGRATE' in os.environ:
+    if isinstance(db.obj, SqliteDatabase) and not 'GENMIGRATE' in os.environ and not 'DB_URI' in os.environ:
         print ('Skipping Sqlite migration!')
         return
 

data/migrations/migration.sh

@@ -5,8 +5,8 @@ up_mysql() {
   docker run --name mysql -p 3306:3306 -e MYSQL_ROOT_PASSWORD=password -d mysql
 
   # Sleep for 5s to get MySQL get started.
-  echo 'Sleeping for 5...'
-  sleep 5
+  echo 'Sleeping for 10...'
+  sleep 10
 
   # Add the database to mysql.
   docker run --rm --link mysql:mysql mysql sh -c 'echo "create database genschema" | mysql -h"$MYSQL_PORT_3306_TCP_ADDR" -P"$MYSQL_PORT_3306_TCP_PORT" -uroot -ppassword'

data/migrations/versions/204abf14783d_add_log_entry_kind_for_verbs.py

@@ -0,0 +1,28 @@
+"""Add log entry kind for verbs
+
+Revision ID: 204abf14783d
+Revises: 2430f55c41d5
+Create Date: 2014-10-29 15:38:06.100915
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = '204abf14783d'
+down_revision = '2430f55c41d5'
+
+from alembic import op
+import sqlalchemy as sa
+
+def upgrade(tables):
+    op.bulk_insert(tables.logentrykind,
+    [
+        {'id': 46, 'name':'repo_verb'},
+    ])
+
+
+def downgrade(tables):
+    op.execute(
+        (tables.logentrykind.delete()
+            .where(tables.logentrykind.c.name == op.inline_literal('repo_verb')))
+
+    )

data/migrations/versions/2430f55c41d5_calculate_uncompressed_sizes_for_all_.py

@@ -16,7 +16,9 @@ from util.uncompressedsize import backfill_sizes_from_data
 
 
 def upgrade(tables):
-  backfill_sizes_from_data()
+  # Note: Doing non-alembic operations inside alembic can cause a deadlock. This call has been
+  # moved to runmigration.sh.
+  pass
 
 def downgrade(tables):
   pass

data/migrations/versions/313d297811c4_add_an_index_to_the_docker_image_id_.py

@@ -0,0 +1,26 @@
+"""Add an index to the docker_image_id field
+
+Revision ID: 313d297811c4
+Revises: 204abf14783d
+Create Date: 2014-11-13 12:40:57.414787
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = '313d297811c4'
+down_revision = '204abf14783d'
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import mysql
+
+def upgrade(tables):
+    ### commands auto generated by Alembic - please adjust! ###
+    op.create_index('image_docker_image_id', 'image', ['docker_image_id'], unique=False)
+    ### end Alembic commands ###
+
+
+def downgrade(tables):
+    ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index('image_docker_image_id', table_name='image')
+    ### end Alembic commands ###

data/migrations/versions/43e943c0639f_add_log_kind_for_regenerating_robot_.py

@@ -12,7 +12,6 @@ down_revision = '82297d834ad'
 
 from alembic import op
 import sqlalchemy as sa
-from sqlalchemy.dialects import mysql
 
 def upgrade(tables):
     op.bulk_insert(tables.logentrykind,

data/migrations/versions/4fdb65816b8d_add_brute_force_prevention_metadata_to_.py

@@ -17,7 +17,7 @@ from sqlalchemy.dialects import mysql
 def upgrade(tables):
     ### commands auto generated by Alembic - please adjust! ###
     op.add_column('user', sa.Column('invalid_login_attempts', sa.Integer(), nullable=False, server_default="0"))
-    op.add_column('user', sa.Column('last_invalid_login', sa.DateTime(), nullable=False, server_default=sa.func.now()))
+    op.add_column('user', sa.Column('last_invalid_login', sa.DateTime(), nullable=False))
     ### end Alembic commands ###