Merge branch 'master' into fix_links_on_sample_page

.rubocop_todo.yml

@@ -53,6 +53,18 @@ AllCops:
 Metrics/MethodLength:
   Enabled: false
 
+ModuleLength:
+  Enabled: false
+
+ClassLength:
+  Enabled: false
+
+Metrics/CyclomaticComplexity:
+  Enabled: false
+
+Metrics/PerceivedComplexity:
+  Enabled: false
+
 Metrics/BlockLength:
   Enabled: false
 

README.md

@@ -15,6 +15,26 @@ Then open `http://localhost:3000` in your browser.
 Everything you need to get started should be in `./bin/setup`.   If there's anything missing, please edit and submit a pull request.
 
 
+## User account logins
+
+In development environment, you can use the following credentials to login for all the non-read operations:
+
+```
+  email: fake@example.com
+  password: password
+```
+
+After you deploy the code, you will have to log into the rails console into the cluster and create a user credential as follows:
+
+```
+idseq-web yf$ bin/shell <cluster> "rails c"
+Running via Spring preloader in process 2608
+Loading alpha environment (Rails 5.1.4)
+irb(main):001:0> User.create(email: 'your@email.com', password: 'yourpass', password_confirmation: 'yourpass', authentication_token: 'your_auth_token')
+```
+
+You can then log in with the emaill/password you specified.
+
 ## Testing
 
 ```
@@ -70,7 +90,7 @@ In addition to using your local `development` instance, you may obtain access to
 1. `chmod 600 idseq_<env>_key.pem`
 1. `ssh-add idseq_<env>_key.pem`
 
-You can now run a non-interactive command on a cloud web container like so  
+You can now run a non-interactive command on a cloud web container like so
 `bin/clam <env> 'echo $HOSTNAME'`
 
 
@@ -89,11 +109,11 @@ Sometimes you may be prompted to run a migration or configuration command like `
 
 ## DB backup/restore within and across environments
 
-1. Backup your local `development` DB into a local file:  
+1. Backup your local `development` DB into a local file:
 `docker-compose exec web mysqldump -h db -u root idseq_development > idseq_development.sql`
-1. Backup cloud `alpha` DB into a local file:  
+1. Backup cloud `alpha` DB into a local file:
 `bin/clam alpha 'mysqldump -h $RDS_ADDRESS -u $DB_USERNAME --password=$DB_PASSWORD idseq_alpha | gzip -c' | gzip -dc > idseq_alpha.sql`
-1. Overwrite your local `development` DB with data from given backup file:  
+1. Overwrite your local `development` DB with data from given backup file:
 `docker-compose run web "cat idseq_alpha.sql | mysql -h db -u root --database idseq_development"`
 
 

app/controllers/reports_controller.rb

@@ -13,9 +13,7 @@ def index
   def show
     @report_details = report_details(@report)
     @view_level = params[:view_level] ? params[:view_level].downcase : 'genus'
-    taxon_zscores = compute_taxon_zscores(@report)
-    @taxonomy_details = taxonomy_details(@view_level, @report, params, taxon_zscores)
-    @highest_tax_counts = highest_tax_counts(@view_level, @report, taxon_zscores)
+    @highest_tax_counts, @taxonomy_details = taxonomy_details(@view_level, @report, params)
   end
 
   # GET /reports/new

app/lib/report_helper.rb

@@ -1,11 +1,10 @@
-# rubocop:disable ModuleLength
 module ReportHelper
   def external_report_info(report, view_level, params)
-    taxon_zscores = compute_taxon_zscores(report)
     data = {}
     data[:report_details] = report_details(report)
-    data[:taxonomy_details] = taxonomy_details(view_level, report, params, taxon_zscores)
-    data[:highest_tax_counts] = highest_tax_counts(view_level, report, taxon_zscores)
+    htc, td = taxonomy_details(view_level, report, params)
+    data[:highest_tax_counts] = htc
+    data[:taxonomy_details] = td
     data[:view_level] = view_level
     data
   end
@@ -33,53 +32,63 @@ def compute_taxon_zscores(report)
     zscore_array
   end
 
-  def taxonomy_details(view_level, _report, params, taxon_zscores)
-    sz = select_zscore(view_level, taxon_zscores)
+  def taxonomy_details(view_level, report, params)
+    taxon_zscores = compute_taxon_zscores(report)
+    wanted_level = view_level == 'species' ? TaxonCount::TAX_LEVEL_SPECIES : TaxonCount::TAX_LEVEL_GENUS
+    data = taxon_zscores.group_by { |h| h[:tax_level] == wanted_level && h[:hit_type] }
+    nt = data['NT'] || []
+    nr = data['NR'] || []
+    htc = highest_tax_counts(nt, nr)
     # filter and sort the nt_scores
-    sort_report!(sz[:nt_zscores], params[:sort_by])
-    rp = resolve_params(params)
-    sz[:nt_zscores].keep_if do |h|
+    rp = resolve_params(params, htc)
+    nt.keep_if do |h|
       (h[:tax_id] >= 0 &&
         h[:zscore] >= rp[:nt_zscore_threshold][:start] &&
-        h[:zscore] < rp[:nt_zscore_threshold][:end] &&
+        h[:zscore] <= rp[:nt_zscore_threshold][:end] &&
         h[:rpm] >= rp[:nt_rpm_threshold][:start] &&
-        h[:rpm] < rp[:nt_rpm_threshold][:end]
+        h[:rpm] <= rp[:nt_rpm_threshold][:end]
       )
     end
-    # cross-references nr_zscores by taxon id
-    nr_zscore_by_taxon = {}
-    sz[:nr_zscores].each do |h|
-      nr_zscore_by_taxon[h[:tax_id]] = h
-    end
-    # pull nt and nr scores for each taxon in order sorted above
+    sort_report!(nt, params[:sort_by])
+    nr_zscore_by_taxon = nr.group_by { |h| h[:tax_id] }
     tax_details = []
-    sz[:nt_zscores].each do |h|
-      tax_details.push(nt_ele: h, nr_ele: nr_zscore_by_taxon[h[:tax_id]])
+    nt.each do |h|
+      x = nr_zscore_by_taxon[h[:tax_id]]
+      tax_details.push(nt_ele: h, nr_ele: x && x[0])
     end
-    tax_details
+    [htc, tax_details]
   end
 
-  def resolve_params(params)
+  def resolve_params(params, data_ranges)
     new_params = {}
     [:nt_zscore_threshold, :nt_rpm_threshold].each do |k|
-      s, e = params[k] ? params[k].split('-') : []
+      s, e = params[k] ? params[k].split(',') : []
+      ntnr, metric, _threshold = k.to_s.split "_"
+      dr_s = data_ranges[('lowest_' + ntnr + "_" + metric).to_sym]
+      dr_e = data_ranges[('highest_' + ntnr + "_" + metric).to_sym]
       new_params[k] = {
-        start: Float(s || -1_000_000_000),
-        end: Float(e || 1_000_000_000) + 1.0
+        start: Float(s || dr_s),
+        end: Float(e || dr_e)
       }
     end
     new_params
   end
 
-  def highest_tax_counts(view_level, _report, taxon_zscores)
-    sz = select_zscore(view_level, taxon_zscores)
-    nt = sz[:nt_zscores]
-    nr = sz[:nr_zscores]
+  def highest_tax_counts(nt, nr)
+    nt_z = nt.map { |h| h[:zscore] }.sort
+    nr_z = nr.map { |h| h[:zscore] }.sort
+    nt_rpm = nt.map { |h| h[:rpm] }.sort
+    nr_rpm = nr.map { |h| h[:rpm] }.sort
     {
-      highest_nt_zscore: nt.map { |h| h[:z_score] }.sort[-1] || 0,
-      highest_nr_zscore: nr.map { |h| h[:z_score] }.sort[-1] || 0,
-      highest_nt_rpm: nt.map { |h| h[:rpm] }.sort[-1] || 0,
-      highest_nr_rpm: nr.map { |h| h[:rpm] }.sort[-1] || 0
+      # if you change keys here, update data_ranges[...] in resolve_params(...)
+      lowest_nt_zscore: nt_z[0] || 0,
+      lowest_nr_zscore: nr_z[0] || 0,
+      lowest_nt_rpm: nt_rpm[0] || 0,
+      lowest_nr_rpm: nr_rpm[0] || 0,
+      highest_nt_zscore: nt_z[-1] || 0,
+      highest_nr_zscore: nr_z[-1] || 0,
+      highest_nt_rpm: nt_rpm[-1] || 0,
+      highest_nr_rpm: nr_rpm[-1] || 0
     }
   end
 
@@ -92,20 +101,6 @@ def sort_report!(nt_zscores, sort_by)
     nt_zscores
   end
 
-  def select_zscore(level, zscores)
-    wanted_level = level == :species ? TaxonCount::TAX_LEVEL_SPECIES : TaxonCount::TAX_LEVEL_GENUS
-    result = {
-      nr_zscores: [],
-      nt_zscores: []
-    }
-    zscores.each do |z|
-      next unless z[:tax_level] == wanted_level
-      t =  z[:hit_type] == :NR || z[:hit_type] == "NR" ? :nr_zscores : :nt_zscores
-      result[t].push(z)
-    end
-    result
-  end
-
   def compute_rpm(count, total_reads)
     if count
       count * 1e6 / total_reads.to_f
@@ -118,7 +113,7 @@ def compute_zscore(rpm, mean, stdev)
     if rpm && stdev && stdev != 0
       (rpm - mean) / stdev
     elsif rpm
-      1e6
+      100
     else
       0
     end

app/models/sample.rb

@@ -1,6 +1,6 @@
 require 'open3'
 require 'json'
-# rubocop:disable ClassLength
+
 class Sample < ApplicationRecord
   self.per_page = 10
   STATUS_CREATED  = 'created'.freeze