Optional email for batch jobs from webservices

Fix default service locations

This should have been in #70

Process batch jobs grouped by email address

We previously processed batch jobs round robin, i.e., one item
for each job per round. This is fair from the job point of view,
but not from the user point of view when one user has many jobs.

We now process batch jobs one item for each user per round,
where we pick the oldest job if a user has more than one. Users
are defined by their email address.

Batch jobs submitted via the webservices all have the same email
address, so they are effectively throttled as if all from the
same user. Adapting the webservices to also allow setting an
email address is future work.

Use interval binning scheme on transcript mappings

This speeds up lookup of transcript mappings by genomic position
a lot. By filtering on bin index, such a query now uses the index
on the bin column, where previously this would involve a
sequential table scan.

http://interval-binning.readthedocs.org/

Back translate

Refactor transcript-protein links to raise NoLinkError instead of None

Never load MUTALYZER_SETTINGS in tests

Documentation updates

Optionally include versions in transcript-protein links

Cache transcript protein links in Redis

Caching of transcript protein links received from the NCBI Entrez
service is a typical use case for Redis. This implements this cache
in Redis and removes all use of our original database table.

An Alembic migration copies all existing links from the database to
Redis. The original `TranscriptProteinLink` database table is not
dropped. This will be done in a future migration to ensure running
processes don't error and to provide a rollback scenario.

We also remove the expiration of links (originally defaulting to 30
days), since we don't expect them to ever change. Negative links
(caching a 'not found' result from Entrez) *are* still expiring,
but with a longer default of 30 days (was 5 days).

The configuration setting for the latter was renamed, yielding the
following changes in the default configuration settings.

Removed default settings:

    # Expiration time for transcript<->protein links from the NCBI (in seconds).
    PROTEIN_LINK_EXPIRATION = 60 * 60 * 24 * 30

    # Expiration time for negative transcript<->protein links from the NCBI (in
    # seconds).
    NEGATIVE_PROTEIN_LINK_EXPIRATION = 60 * 60 * 24 * 5

Added default setting:

    # Cache expiration time for negative transcript<->protein links from the NCBI
    # (in seconds).
    NEGATIVE_LINK_CACHE_EXPIRATION = 60 * 60 * 24 * 30

Create new Redis connection when REDIS_URI changes

When the REDIS_URI configuration setting is changed, the Redis
client should be reconfigured with a new connection pool, just
like we do with the database.

It appears redis-py manages the connection pool by itself and
doesn't expose ways to explicitely destroy it or close all
connections (this is done automatically when all connections
loose scope).

This fix ensures that the unit tests don't accidentally work on
the Redis database configured in MUTALYZER_SETTINGS, which was
quite an unfortunate bug.

Remove debug statement

Add protein_to_transcript in separate ncbi module

Jeroen F.J. Laros authored 9 years ago and Vermaat committed 9 years ago

Existing `transcript_to_protein` is factored out into a separate
`mutalyzer.ncbi` module.

Add Ter as a valid AA in the HGVS grammar

Previously, the `PSubst` rule did not register `MutationType`, so it
was a bit awkward how to check for a `p.` substitution. We can now:

    >>> grammar.parse('NP_00011.1:p.Asp23Tyr').RawVar.MutationType
    'subst'