Commit dd2f53d2 authored by bow's avatar bow
Browse files

Update history.rst for 0.2.0 version

parent a43180b5
......@@ -2,15 +2,77 @@ History
Releases 0.2
Version 0.2
Version 0.2.0
Release 0.2.0
`release date: TBD`
Release 0.2.0-beta1
`release date: January 25 2016`
First beta release of the 0.2 version.
The majority of the change in this version compared to the previous version
is internal. Some of the more important changes are:
* The ``sentinel`` package has now been split into ``sentinel``,
containing generic functionalities and ``sentinel-lumc`` containing
LUMC-specific pipeline support. This separation is not yet complete,
since a part of the user configuration still refers to LUMC-specific
functionalities. Instead, it is meant to pave way for a complete
separation which is expected to happen in future versions.
* A new type for expected errors called ``ApiPayload`` was created to
replace the previous ``ApiMessage`` case class which contains only
error messages. In addition to error messages, ``ApiPayload`` may also
contain a function that returns a specific HTTP error code. This allows
for a given error message to always be tied to a specific HTTP error
* The main pipeline upload processing function in ``RunsProcessorr``
has been renamed to ``processRunUpload`` and is now expected to return
``Future[ApiPayload \/ RunRecord]`` instead of ``Try[BaseRunRecord]``.
Related to this change, this version also makes heavier use of the
scalaz library, most notably its disjunction type. This allows for a
nicer composition with ``Future``, which has resulted in changes across
database-related functions to use ``Future`` as well.
* The base functions in the ``StatsProcessor`` abstract class underwent
a major refactor. In this version, the same functionality was achieved
using only two generic classes ``getStats`` and ``getAggregateStats``.
Future versions are expected to bring additional changes most notably
to the MapReduce step, since newer versions of MongoDB supports most
(if not all) of the metrics using its aggregation framework only.
There are also some indirect changes related to the code:
* Sentinel now comes with minimum deployment setup using Ansible. This can
be optionally run in a Vagrant VM with the provided Vagrantfile.
* The required MongoDB version is now 3.2 instead of 3.0.
The complete list of changes are available in the commit logs.
The user-visible changes are quite minimum. Aside from some LUMC
pipeline-specific changes, the most visible changes are:
* The `library` nomenclature has been replaced with `read group`. The
previous use of `library` was incorrect and the current one is more
in-line with popular next-generation sequencing tools.
* There is now a URL-parameter called ``displayNull`` which allows for
clients to view missing JSON attributes as ``null`` when this value is
set to ``true``. When set to ``false``, which is the default value,
missing attributes will be omitted completely from the returned JSON
Version 0.1
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment