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NCS Navigator MDES Warehouse

MDES Warehouse is the central collation and reporting engine for the NCS Navigator suite. It provides the infrastructure to support transforming data from the operational and data-collection systems and converting it into the format required for reporting to the National Children's Study program office.

While it has been built for the NCS Navigator suite, it exposes generic attachment points for transformers, potentially allowing it to be used with other sets of transactional systems for the National Children's Study.

System Requirements

MDES Warehouse is installed as a ruby gem. It's compatible with Ruby 1.8.7 (including REE) and 1.9.2. It relies on PostgreSQL 9 (or later).

Set up

Install the gem

$ gem install ncs_mdes_warehouse

This will install the gem, all its dependencies, and the mdes-wh executable.

Set the environment

The warehouse detects the kind of environment it's running in (production, staging, or development) via the NCS_NAVIGATOR_ENV environment variable. Arrange for this variable to be set to an appropriate value for the server where you're deploying the warehouse:

# In, e.g., /etc/bashrc
export NCS_NAVIGATOR_ENV=staging

If you're deploying on a workstation (i.e., for development) you can skip this step -- the default environment is development.

Configure the NCS Navigator suite

If you haven't already, create /etc/nubic/ncs/navigator.ini by following the example in the ncs_navigator_configuration gem.

Create the PostgreSQL databases

The warehouse requires two PostgreSQL databases. There are several ways to create them. createdb is one:

$ createuser -e -h dbserver.my.org -PRSD mdes_warehouse
Enter password for new role:
Enter it again:
CREATE ROLE mdes_warehouse PASSWORD 'md5...' NOSUPERUSER NOCREATEDB NOCREATEROLE INHERIT LOGIN;
$ createdb -e -O mdes_warehouse mdes_warehouse_working
CREATE DATABASE mdes_warehouse_working OWNER mdes_warehouse;
$ createdb -e -O mdes_warehouse mdes_warehouse_reporting
CREATE DATABASE mdes_warehouse_reporting OWNER mdes_warehouse;

Additional database roles

For safe reporting purposes, the warehouse automatically creates PII-screened views in a schema named no_pii. Since those views are dropped along with everything else when the warehouse schema is recreated, direct grants from user accounts to to the views will be lost every time ETL runs. To work around this potential problem, the schema creation process looks for a role named mdes_warehouse_no_pii. If this role exists, it will be granted read-only access to these PII-screened views. Here's how you can create the role:

$ createuser -e -h dbserver.my.org -LRSD mdes_warehouse_no_pii
CREATE ROLE mdes_warehouse_no_pii NOSUPERUSER NOCREATEDB NOCREATEROLE INHERIT NOLOGIN;

Individual data analyst accounts can then be granted this role to have access to a PII-free view of the warehouse:

# In a database console
GRANT mdes_warehouse_no_pii TO some_data_analyst;
# Following is optional; it will make sure that some_data_analyst
# will default to querying the PII-free views instead of the
# (inaccessible) full-data tables in the public schema.
ALTER some_data_analyst SET search_path=no_pii;

Configure bcdatabase

Like the rest of the NCS Navigator suite, MDES Warehouse uses bcdatabase to locate database access parameters and credentials. Bcdatabase looks for credentials under /etc/nubic/db. The specific file that the warehouse looks in will depend on the environment in which you're running:

  • development: local_postgresql.yml
  • staging: ncsdb_staging.yml
  • production: ncsdb_prod.yml

Create or update the appropriate file with the warehouse configuration for your environment. The below is an example; yours may differ. The MDES Warehouse-specifc parts are the datamapper_adapter configuration key and the two mdes_warehouse_* entries.

defaults:
  host: ncsdb-staging.my.org
  adapter: postgresql
  datamapper_adapter: postgres
mdes_warehouse_working:
  username: mdes_warehouse
  password: whatever-i-entered-before
mdes_warehouse_reporting:
  username: mdes_warehouse
  password: whatever-i-entered-before

Configure warehouse

The warehouse takes its base configuration from a file under the directory /etc/nubic/ncs/warehouse. The name of the file should be ${NCS_NAVIGATOR_ENV}.rb; e.g., for the production environment, the full path would be /etc/nubic/ncs/warehouse/production.rb.

The minimum contents of this file is a list of transformers, which are components that translate data from some source system or systems:

c.add_transformer VdrXml.from_most_recent_file(c, Dir['/var/lib/ncs/mdes/COOK*.xml'])
c.add_transformer StaffPortal.create_transformer(c)

The warehouse includes some transformers. Others are included with the NCS Navigator suite applications themselves. See below for more information (TODO).

The warehouse configuration file may optionally include other overrides to MDES warehouse defaults. See the {file:sample_configuration.rb} for details.

Verify your settings

You can verify most of these settings by running this command:

$ mdes-wh create-schema

It will connect to the working database and create a schema matching the current MDES version.

TODO: a more complete verification utility.

Use

MDES Warehouse provides an executable named mdes-wh which has several subcommands. To get a list of the commands, use mdes-wh help.

Monitoring

The warehouse produces interactive monitoring output on standard error for most of its actions. This output can be suppressed using the --quiet command line option, or by setting c.output_level = :quiet in the environment config file.

Separately, warehouse actions are more permanently logged in a log file. The log file name defaults to /var/log/ncs/warehouse/{env_name}.log and can be changed in the environment configuration file. This log file is never cleaned out automatically; consider using logrotate or a similar tool to rotate it on a daily or weekly basis.

If a log can't be written to (e.g., because the directory doesn't exist), the warehouse will dump warnings and errors to standard out instead. The log file will contain more detail than the messages dumped to standard out, so don't rely on this backup behavior in production.