Add gitignore

Signed-off-by: Byron Ruth <b@devel.io>
Add DCC documentation repo as submodule

Signed-off-by: Byron Ruth <b@devel.io>
Define pedsnet package

pedsnet package contains utilities for processing input data from
sites in the sanctioned formats, staging it, and merging it into the
target production database.

The pedsnet.omop package contains the minimal Django-based data models
for supporting the pedsnet.etl package.

Signed-off-by: Byron Ruth <b@devel.io>
Fix DataArchive state numbering

Signed-off-by: Byron Ruth <b@devel.io>
Implement `pedsnet.db` module for creating on-demand databases

This is to support creating staging databases for data archives.

Signed-off-by: Byron Ruth <b@devel.io>
Remove foreign key constraints and allow for more nulls

Signed-off-by: Byron Ruth <b@devel.io>
Update metadata fields to include `org_name`

Signed-off-by: Byron Ruth <b@devel.io>
Change primary key fields to be auto-incrementing

This is primarily for testing purposes since the staging data will
already contain primary keys and the warehouse is managed externally.

Signed-off-by: Byron Ruth <b@devel.io>
Implement limited set of OMOP model processors

This is a very basic implementation and does not include any
optimizations such as caching or parallelization.

Signed-off-by: Byron Ruth <b@devel.io>
Refactor and optimize OMOP push processors

These changes pre-cache a mapping of natural keys to instance data
which drives the behavior of the processor.

Signed-off-by: Byron Ruth <b@devel.io>
Add convenience method on DataArchive to push staged data

Signed-off-by: Byron Ruth <b@devel.io>
Ensure connections are closed on database drop

Add a short max age for staging databases connections to prevent them
dangling around in case they are not closed properly.

Signed-off-by: Byron Ruth <b@devel.io>
Add stage command

Signed-off-by: Kevin Murphy <murphyke@email.chop.edu>
Merge pull request #5 from PEDSnet/issue-3-kev

Implement DataArchive.stage and command
Add more null, remove blank arguments

Signed-off-by: Byron Ruth <b@devel.io>
Set database name on creation since it is static

The stage of the archive is defined by the state it is in. Having the
database name set does not imply the database is staged.

Signed-off-by: Byron Ruth <b@devel.io>
Improve validation check of file by attempting to open

Previously, the test only checked if the file existed.

Signed-off-by: Byron Ruth <b@devel.io>
Add assertion of data in staging test

Signed-off-by: Byron Ruth <b@devel.io>
Fix file_digest and is_utf8 chunk reading

Signed-off-by: Byron Ruth <b@devel.io>
Replace stdout message to debug logging

Signed-off-by: Byron Ruth <b@devel.io>