Create test for allele frequency calculation

Signed-off-by: Ryan O'Hara <oharar@email.chop.edu>
Merge pull request #246 from ryanjohara/allele-freq-test

Create test for allele frequency calculation
Fixed Issue #125 puppet step to add iptable rule

Signed-off-by: Sheik Hassan <solergiga@yahoo.com>
Optimize the SolveBio ClinVar query to prevent slow variant resource requests

Remove the by-gene filter to narrow down the result sets and return only the first 10 results from the query.
Adds the total result count to the clinvar dictionary in the variant resource. Also fixes an issue with the genomic position filter.

Signed-off-by: David Caplan <dcaplan@gmail.com>
Merge pull request #241 from solvebio/solvebio-speed

Optimize the SolveBio ClinVar query to prevent slow variant resource requests
Use less severe log level when skipping gene rank records

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Merge pull request #232 from muslimgiga/master

Add iptables rule to puppet script to allow 0.0.0.0:8000
Enable eqeqeq in jshintrc
Added protein change information in details view

Signed-off-by: Sheik Hassan <solergiga@yahoo.com>

Signed-off-by: Sheik Hassan <solergiga@yahoo.com>
Merge pull request #250 from muslimgiga/issue-248

Fix #248.

Added protein change information to the amino acid changes in details view
Add Sample concept with Project and Sample fields

This also squashes all the redundant avocado metadata migrations and fixtures into a single one using the most recent fixture after the new Sample concept was created

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Fixed Bug with gene resources

Signed-off-by: Sheik Hassan <solergiga@yahoo.com>
Merge pull request #256 from muslimgiga/issue-247

Fix #247
Merge pull request #255 from cbmi/issue-172

Add Sample concept with Project and Sample fields
Add missing bindings for knowledge capture save handlers

This fixes the problems where the success/error notifications where not working.

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Fix bug where knowledge capture form was always unpopulated

Due to a recent change in Backbone(https://github.com/jashkenas/backbone/pull/2878) we need to set id on the attributes not on model.id directly

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Merge pull request #259 from cbmi/knowledge-capture

Fix bugs in knowledge capture form and save notification system
Replace deprecated query.concepts.required with filters.required

This was updated in Cilantro 2.2.25. This insures compatibility with
future versions of Cilantro once the old query.concepts.required config
option is removed altogether.

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Do not assume read depth is present in pipeline checks

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Use __name__ over __file__ in queue logger