Midstream

alembic.ini

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+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = alembic
+
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+sqlalchemy.url = postgresql://mercy:mercy@postgresql.aklabs.net/mercy
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

alembic/README

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+Generic single-database configuration.

alembic/env.py

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+from __future__ import with_statement
+from alembic import context
+from sqlalchemy import engine_from_config, pool
+from logging.config import fileConfig
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+target_metadata = None
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+def run_migrations_offline():
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(url=url)
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    engine = engine_from_config(
+                config.get_section(config.config_ini_section),
+                prefix='sqlalchemy.',
+                poolclass=pool.NullPool)
+
+    connection = engine.connect()
+    context.configure(
+                connection=connection,
+                target_metadata=target_metadata
+                )
+
+    try:
+        with context.begin_transaction():
+            context.run_migrations()
+    finally:
+        connection.close()
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()
+

alembic/script.py.mako

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+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision}
+Create Date: ${create_date}
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+def upgrade():
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+    ${downgrades if downgrades else "pass"}

alembic/versions/58f6a99bd6ec_create_fda_product_t.py

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+"""create fda_product table
+
+Revision ID: 58f6a99bd6ec
+Revises: None
+Create Date: 2013-10-19 21:21:03.977000
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = '58f6a99bd6ec'
+down_revision = None
+
+from alembic import op
+import sqlalchemy as sa
+
+
+def upgrade():
+    op.create_table(
+        'fda_products',
+        sa.Column('id', sa.String, primary_key=True),
+        sa.Column('ndc', sa.String, nullable=False),
+        sa.Column('type', sa.String, nullable=False),
+        sa.Column('proprietaryName', sa.String, nullable=False, index=True),
+        sa.Column('proprietaryNameSuffix', sa.String),
+        sa.Column('genericName', sa.String, nullable=False),
+        sa.Column('marketingCategoryName', sa.String, nullable=False),
+        sa.Column('labelerName', sa.String, nullable=False)
+        sa.Column('deaSchedule', sa.String, nullable=False)
+        )
+    op.create_table(
+        'fda_product_substances',
+        sa.Column('fda_product_id',
+                  sa.String,
+                  ForeignKey('fda_products.id'),
+                  nullable=False),
+        sa.Column('substanceName', sa.String, nullable=False),
+        sa.Column('strengthNumber', sa.String, nullable=False),
+        sa.Column('strengthUnit', sa.String, nullable=False),
+        sa.Column('pharmaClasses', sa.String, nullable=False)
+        )
+    op.create_table(
+        'drugbank_drugs',
+        sa.Column('id', sa.String, primary_key=True, unique=True),
+        sa.Column('name', sa.String, nullable=False, index=True),
+        sa.Column('indication', sa.String, nullable=False),
+        sa.Column('ndc_id', sa.String, ForeignKey('fda_products.id'), nullable=True),
+        sa.Column('wikipedia', sa.String, nullable=True)
+        )
+    op.create_table(
+        'drugbank_prices',
+        sa.Column('id', sa.String, ForeignKey('drugbank_drugs.id'), nullable=False),
+        sa.Column('description', sa.String, nullable=False),
+        sa.Column('currency', sa.String, nullable=False),
+        sa.Column('cost', sa.Float, nullable=False, index=True)
+        sa.Column('unit', sa.String, nullable=False)
+        )
+    op.create_table(
+        'drugbank_categories',
+        sa.Column('id', sa.Integer, primary_key=true, autoincrement=True),
+        sa.Column('name', sa.String, nullable=False)
+        )
+    op.create_table(
+        'drugbank_drug_categories',
+        sa.Column('id', sa.String, ForeignKey('drugbank_drugs.id'), nullable=False),
+        sa.Column('category_id', sa.Integer, ForeignKey('drugbank_categories.id'), nullable=False)
+        )
+    op.create_table(
+        'drugbank_packagers',
+        sa.Column('id', sa.String, ForeignKey('drugbank_drugs.id'), nullable=False),
+        sa.Column('name', sa.String, nullable=False),
+        sa.Column('url', sa.String, nullable=False)
+        )
+    op.create_table(
+        'drugbank_manufacturers',
+        sa.Column('id', sa.String, ForeignKey('drugbank_drugs.id'), nullable=False),
+        sa.Column('name', sa.String, nullable=False),
+        sa.Column('generic', sa.Boolean, nullable=False)
+        )
+    op.create_table(
+        'drugbank_genericnames',
+        sa.Column('id', sa.String, ForeignKey('drugbank_drugs.id'), nullable=False),
+        sa.Column('name', sa.String, index=True, nullable=False)
+        )
+    op.create_table(
+        'drugbank_synonyms',
+        sa.Column('id', sa.String, ForeignKey('drugbank_drugs.id'), nullable=False),
+        sa.Column('name', sa.String, index=True, nullable=False)
+        )
+
+def downgrade():
+    pass

alembic/versions/58f6a99bd6ec_create_fda_product_t.py~

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+"""create fda_product table
+
+Revision ID: 58f6a99bd6ec
+Revises: None
+Create Date: 2013-10-19 21:21:03.977000
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = '58f6a99bd6ec'
+down_revision = None
+
+from alembic import op
+import sqlalchemy as sa
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass

puppet/mercy/manifests/#init.pp#

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+class mercy(
+  $environment,
+  $version,
+  $ensure,
+  $rabbitmq_uri,
+  $process_user    => 'mercy',
+  $process_group   => 'mercy',
+  $process_threads => 5,
+  $servername      => $::fqdn,
+  $rabbitmq_user   => 'mercy',
+  $rabbitmq_pw     => 'mercy',
+  $rabbitmq_vhost  => 'mercy',
+  $vhost_dir       => '/etc/apache/httpd/conf.d',
+  $apache_service  => 'httpd',
+  $port            => 443,
+  $postgres_uri    => 'localhost',
+  $postgres_user   => 'mercy',
+  $postgres_pw     => 'mercy',
+  $postgres_db     => 'mercy')
+{
+  if ! defined(User[$process_user]) {
+    user { $process_user:
+      ensure => 'present'
+    }
+  }
+  if ! defined(Group[$process_group]) {
+    user { $process_group:
+      ensure => 'present'
+    }
+  }
+}

puppet/mercy/manifests/init.pp

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+class mercy(
+  $environment,
+  $version,
+  $ensure,
+  $rabbitmq_uri,
+  $process_user    => 'mercy',
+  $process_group   => 'mercy',
+  $process_threads => 5,
+  $servername      => $::fqdn,
+  $rabbitmq_user   => 'mercy',
+  $rabbitmq_pw     => 'mercy',
+  $rabbitmq_vhost  => 'mercy',
+  $vhost_dir       => '/etc/apache/httpd/conf.d',
+  $apache_service  => 'httpd',
+  $port            => 443,
+  $postgres_uri    => 'localhost',
+  $postgres_user   => 'mercy',
+  $postgres_pw     => 'mercy',
+  $postgres_db     => 'mercy')
+{
+             include 'mercy::params'
+}

puppet/mercy/manifests/params.pp

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+class mercy::params
+{
+
+}

puppet/mercy/manifests/params.pp~

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+class mercy::params ( $environment,
+                      $version,
+                      $ensure,
+                      $rabbitmq_uri,
+                      # ---- Everything below is optional
+                      $process_user    => 'mercy',
+                      $process_group   => 'mercy',
+                      $process_threads => 5,
+                      $servername      => $::fqdn,
+                      $rabbitmq_user   => 'mercy',
+                      $rabbitmq_pw     => 'mercy',
+                      $rabbitmq_vhost  => 'mercy',
+                      $vhost_dir       => '/etc/apache/httpd/conf.d',
+                      $apache_service  => 'httpd',
+                      $port            => 443,
+                      $postgres_uri    => 'localhost',
+                      $postgres_user   => 'mercy',
+                      $postgres_pw     => 'mercy',
+                      $postgres_db     => 'mercy'
+                      )
+{
+
+}

puppet/mercy/templates/apache/vhost.erb

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+<VirtualHost * :<%= scope.lookupvar('::mercy::port') %>>
+    ServerName <%= scope.lookupvar('::fqdn') %>
+    WSGIDaemonProcess mercy user=<%= scope.lookupvar('::mercy::process_user') %> group=<%= scope.lookupvar('::mercy::process_group') %> threads=<%= scope.lookupvar('::mercy::process_threads') %>
+    WSGIScriptAlias / /opt/mercy/scripts/mercy.wsgi
+
+    <Directory /opt/mercy>
+	WSGIProcessGroup mercy
+	WSGIApplicationGroup %{GLOBAL}
+	Order deny, allow
+	Allow from all
+    </Directory>
+</VirtualHost>

puppet/mercy/templates/apache/vhost.erb~

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+<VirtualHost *:<%= scope.lookupvar('::mercy::params::port') %>>
+    ServerName <%= scope.lookupvar('::fqdn') %>
+    WSGIDaemonProcess mercy user=<%= scope.lookupvar('::mercy::params::process_user') %> group=<%= scope.lookupvar('::mercy::params::process_group') %> threads=<%= scope.lookupvar('::mercy::params::process_threads') %>
+    WSGIScriptAlias / /opt/mercy/scripts/mercy.wsgi
+
+    <Directory /opt/mercy>
+	WSGIProcessGroup mercy
+	WSGIApplicationGroup %{GLOBAL}
+	Order deny, allow
+	Allow from all
+    </Directory>
+</VirtualHost>

puppet/mercy/templates/python/alembic.ini.erb

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+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = /opt/mercy/alembic
+
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+sqlalchemy.url = postgresql://<%= scope.lookupvar('::mercy::postgres_user') %>:<%+ scope.lookupvar('::mercy::postgres_pw') %>@<%= scope.lookupvar('::mercy::postgres_uri') %>/<%= scope.lookupvar('::mercy::postgres_db') %>
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

puppet/mercy/templates/python/alembic.ini.erb~

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+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = alembic
+
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+sqlalchemy.url = driver://mercy:mercy@postgresql.aklabs.net/mercy
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

scripts/mercy.wsgi

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+from mercy.MercyApplication import MercyApplication
+
+class ScriptNameStripper(object):
+    def __init__(self, app):
+        self.app = app
+
+    def __call_(self, environ, start_response):
+        environ['SCRIPT_NAME'] = ''
+        return self.app(environ, start_response)
+
+app = ScriptNameStripper(MercyApplication())
+
+if __name__ == "__main__":
+    app.run()