update allele indexer with hashmap lookups for status and disease
add procedure group field to store the procedure without the version
add procedure group field to store the procedure without the version
Merge branch 'master' of https://github.com/mpi2/PhenotypeArchive

# By Richard Easty (36) and others
# Via Richard Easty (4) and others
* 'master' of https://github.com/mpi2/PhenotypeArchive: (63 commits)
  removed console
  fixed bug of displaying wrong label for disease_source and disease_classification
  copy preqc_gene_id, which works to mgi_accession_id for now as a test
  one more test with mgi_accession_id by moving its postion in entity preqc2
  test for missing mgi_accession_id with preqc_gene_id field
  fixed latest_phenotype_status for getting the right status for preqc2 entity
  added <field column="latest_phenotype_status" name="latest_phenotype_status" />
  added mgi_accession_id field
  fixed xpath error
  added the bit to index gene fields for mps in preqc core
  comment about facets moved on top of list
  added some viability pie code with some hacks so we see pies without experiment for testing
  removed console
  Add message if not found; fix accession id.
  fixed null problem of mapped hp term
  boosted top_level_mp_term:"reproductive system phenotype" for values that are "female infertility, male infertility and infertility" to top of list on dataTable
  Fix exception.
  Remove makeItem routine.
  Add new order/contact/details routine for summary section.
  use double qf fields to deal with exact and partial string match
  ...
formatting and streamline pivot field specification
remove short circuit favicon code
Merge branch 'master' of https://github.com/mpi2/PhenotypeArchive

# By jwgwarren (3) and others
# Via jwgwarren (2) and others
* 'master' of https://github.com/mpi2/PhenotypeArchive:
  Increase read timeout (MP docs are embiggening)
  more styling and error checking to images comparator
  changed image comparator to show one panel for control or experimental if only one type of image has been selected.
  This change refactors testFacetCounts() and testSpecialCharacters to testFacetCountsNoSearchTerm() and testFacetCountsSpecialCharacters().
  Created a generic PieChartCreator
half way sort out statuses
Merge branch 'master' of https://github.com/mpi2/PhenotypeArchive

# By Richard Easty
# Via Richard Easty
* 'master' of https://github.com/mpi2/PhenotypeArchive:
  Fix /alleles/qc_data/.
  Tidy.
  Tidy; fix qc data; fix tv's.
  add qc data simple layout file
  Fix QC data layout.
  Manage QC Data better.
allow null date_of_birth in live_sample
default sex and zygosity for line level parameters to "not applicable"
do a final commit to ensure all records are written
log error when cannot find biological model for experiment
added support for impcMediaUrl to be obtained from main config in
pom.xml and passed to imageComparator.
somewhere towards viability graph support
Merge branch 'master' of https://github.com/mpi2/PhenotypeArchive.git
changed impcMedia url to relative url
separate click from the rest
Merge branch 'master' of https://github.com/mpi2/PhenotypeArchive

# By jwgwarren
# Via jwgwarren
* 'master' of https://github.com/mpi2/PhenotypeArchive:
  changed impcMedia url to relative url
  somewhere towards viability graph support
  added support for impcMediaUrl to be obtained from main config in pom.xml and passed to imageComparator.
added annotation break between image name and zygosity