Only truncate once before updating frequencies

This fixes a bug where we were only seeing the frequencies being updated for the last cohort in the list. This was a result of the placement of the truncate command. Previously, the truncation happened every loop iteration. Now, it happens before the loop starts.

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Sort genes by effect impact in gene rank command

This also updates the test to be more general with regard to checking
that scores were added.

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Merge pull request #243 from cbmi/issue-238

Only truncate once before updating frequencies
Merge pull request #244 from cbmi/issue-236

Sort genes by effect impact in gene rank command
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
Add Analysis model, links, and migrations

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Add resources for getting analyses and related data

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Add trailing slash to avoid 301 redirect codes

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Return the analysis in the assessment resource data

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Use constants as Analysis statuses for external reference availability

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Add assessment status drop down to knowledge capture tab

This commit also "freezes" the UI when the status of the assessment is complete by disabling all input.

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Add Analysis header link & fix workspace icon

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Move template registration out of main.js

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Trivial implementation of the Analysis workflow

Signed-off-by: Don Naegely <naegelyd@gmail.com>