To support the storage of RNASeq data (readcounts) and the GroupTest analysis on this.
Merge pull request #1 from thehyve/RNASeq

To support the storage of RNASeq data (readcounts) and the GroupTest ana...
Fix putative bug in i2b2_load_clinical_data

For the kind of concepts added, the data type in i2b2 should always
be 'T'.
Add oracle variables to vars.sample
Support Solr core used in Sanofi's Oracle branch

Clean old cores with `make -C solr clean_cores`
and start the Oracle core with `ORACLE=1 make -C solr start`

Maybe we should have separate directories for Oracle/PostgreSQL, so
that we don't have to clean the cores when changing RDBMSs.
Sanofi branch requires a few config overrides

Add a Config-extra.php sample file for this purpose.
Fix ExtractingRequestHandler/Solr Cell
Add/override sanofi specific settings

in its Config-extra.php.sample-sanofi.
Added extra columns to VCF tables, to enable on-the-fly calculations on variants
Support loading of clinical sample data in Oracle

Only clinical data is supported now, but the path is laid for other
types.

Also added support for private studies.

vars file will have to be changed. See vars.sample.
Remove/ignore s/ora/kettle-home/kettle.properties
Add script to show job audit and errors

Invoke with:

    make -C samples/{oracle,postgres} showdblog
Merge branch oracle_kettle into master
Remove stale comment
Support the upload of RNASeq data and it's platform (chromosonal region).
To support the upload of "date" and "units" with observations.
Also grouping of observations through "modifier_cd" possible.
Upgrade to solr 4.5.0
Fix comment and don't process /images/tempImages

Keep /images/tempImages out of the reach of the adhoc resources plugin
Remove extra / from grails.resources.adhoc.excludes
Change prod log file size from 1K to 100M