Merge branch 'develop' into update_capybara-webkit

CHANGELOG.md

@@ -7,8 +7,20 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ## [Unreleased]
 
+### Added
+
 - #643 : Moved `reindex.bety.sh` and `vacuum.bety.sh` scripts from PEcAn to BETY and provided access through entrypoint. 
 
+### Changed
+
+- Documentation updates, now point to new [documentation location](https://pecanproject.github.io/bety-documentation/index.html)
+- #652 : Better list of soil choices
+
+### Fixed
+
+- Updated GEM list to fix security fixes as recommended by dependbot on GitHub.
+
+
 ## [5.2.0] - 2019-03-11
 
 ### Added
@@ -19,7 +31,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ## [5.1.0] - 2019-01-14
 
-### Fixes
+### Fixed
 
 - #611 : could not close alerts
 - #585 : Pressing "Show" on the Covariates Edit page attempts an update
@@ -30,34 +42,34 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ## [5.0.5] - 2018-10-23
 
-### Fixes
+### Fixed
 
 - #603 : Restores Rails route to make method completion work in Bulk Upload Wizard
 
 ## [5.0.4] - 2018-10-11
 
-### Fixes
+### Fixed
 
 - #600 : Error when starting BETY as docker container due to frozen variable.
 
 ## [5.0.3] - 2018-09-28
 
-### Fixes
+### Fixed
 
 - #593 : Replaces references to gitter with references to slack.
-- #598 : Fixes issue in docker where the entrypoint referenced a wrong URL to download the initial schema from.
+- #598 : Fixed issue in docker where the entrypoint referenced a wrong URL to download the initial schema from.
 
 ## [5.0.2] - 2018-08-09
 
-### Fixes
+### Fixed
 - Update to sprockets gem
 
 ## [5.0.1] - 2018-08-08
 
-### Fixes
-- Fixes fuzzy matching used in search queries
+### Fixed
+- Fixed fuzzy matching used in search queries
 
 ## [5.0.0] - 2018-08-07
 
-### Fixes
+### Fixed
 - Major upgrade to rails 5, make sure to read documentation on how to upgrade.

Gemfile.lock

@@ -245,7 +245,7 @@ GEM
     xpath (3.0.0)
       nokogiri (~> 1.8)
     yajl-ruby (1.3.1)
-    yard (0.9.12)
+    yard (0.9.20)
 
 PLATFORMS
   ruby

README.md

@@ -35,7 +35,7 @@ docker run -e RAILS_RELATIVE_URL_ROOT="/bety" pecan/bety
 
 ## Documentation.
 
-* Technical Documentation: https://pecan.gitbooks.io/betydb-documentation/content/
-* Data Entry: https://pecan.gitbooks.io/betydbdoc-dataentry/content/
-* Data Access: https://pecan.gitbooks.io/betydb-data-access/content/
+* Technical Documentation: https://pecanproject.github.io/bety-documentation/technical/
+* Data Entry: https://pecanproject.github.io/bety-documentation/dataentry/
+* Data Access: https://pecan.gitbook.io/betydb-data-access/
 

app/controllers/bulk_upload_controller.rb

@@ -121,7 +121,7 @@ def store_trait_method_mapping_in_session
       method_name: params["method_info"]["label"],
       method_id: params["method_info"]["value"]
     }
-    render(nothing: true)
+    render(body: nil)
   end
 
   # Step 1: Choose a file to upload.

app/models/site.rb

@@ -231,7 +231,7 @@ def city_state
 
   def sitename_state_country
     output = ""
-    
+
     #city = city.chomp if !city.nil?
     if !sitename.blank?
       output += "#{sitename}"
@@ -262,6 +262,17 @@ def autocomplete_label
     "#{sitename.squish} (#{city.squish}, #{!(state.nil? || state.empty?) ? " #{state.squish}," : ""} #{country.squish})"
   end
 
+  ### Class methods
+
+  def self.soil_classes
+
+    @soil_classes ||= ['clay', 'clay loam', 'loam', 'loamy sand', 'sand',
+                       'sandy clay', 'sandy clay loam', 'sandy loam',
+                       'silt', 'silt loam', 'silty clay', 'silty clay loam',
+                       'peat', 'bedrock', 'other'].freeze
+  end
+
+
   private
 
   ## Validation methods

app/views/layouts/application.html.erb

@@ -200,9 +200,9 @@
 
             <li class="menu-docs"> <a>Docs</a>
               <ul class="sub-menu">
-                <li><%= link_to "Data Entry", "https://pecanproject.github.io/bety-documentation/dataentry/", :target =>"_blank" %></li>
-                <li><%= link_to "Data Access", "https://pecan.gitbooks.io/betydb-data-access/content/", :target =>"_blank" %>></li>
-                <li><%= link_to "Implementation", "https://pecanproject.github.io/bety-documentation/technical", :target =>"_blank" %></li>
+                <li><%= link_to "Data Entry", "https://pecanproject.github.io/bety-documentation/dataentry", :target =>"_blank" %></li>
+                <li><%= link_to "Data Access", "https://pecan.gitbook.io/betydb-data-access/", :target =>"_blank" %>></li>
+                <li><%= link_to "Implementation", "https://pecanproject.github.io/bety-documentation/technical/", :target =>"_blank" %></li>
                 <li><%= link_to "Schema", schemas_path %>></li>
               </ul>
             </li>
@@ -292,7 +292,7 @@
           <h3><strong>BETY</strong>db</h3>
           <ul class="unstyled">
                       <li><%= link_to "Homepage", root_path %></li>
-                      <li><%= link_to "Documentation", "https://pecan.gitbooks.io/betydb-documentation/content/", :target =>"_blank" %></li>
+                      <li><%= link_to "Documentation", "https://pecanproject.github.io/bety-documentation/", :target =>"_blank" %></li>
                       <% if CONFIG[:show_crop_map_links] %>
                       <li><%= link_to "Maps & Data", maps_path %></li>
                       <% end %>

app/views/sites/edit.html.erb

@@ -311,7 +311,7 @@
             <%= f.label :lon %>
             <%= geometry_aware_text_field(f, :lon, { class: "input-full" }) %>
             <%= f.label :soil %>
-            <%= f.select :soil, %w(sandloamy sandsandy loamsilt loamloamsandy clay loamsilty clay loamclay loamsandy claysilty clayclaypeat), { :include_blank => true }, :class => "input-full" %>
+            <%= f.select :soil, Site.soil_classes, { :include_blank => true }, :class => "input-full" %>
 
             <div class="two columns alpha">
               <%= f.label :clay_pct, "% Clay" %>

app/views/sites/new.html.erb

@@ -309,7 +309,7 @@
             <%= f.text_field :lon, :class => "input-full" %>
             <br /><br />
             <%= f.label :soil %>
-            <%= f.select :soil, %w(sandloamy sandsandy loamsilt loamloamsandy clay loamsilty clay loamclay loamsandy claysilty clayclaypeat), { :include_blank => true }, :class => "input-full" %>
+            <%= f.select :soil, Site.soil_classes, { :include_blank => true }, :class => "input-full" %>
 
             <div class="two columns alpha">
               <%= f.label :clay_pct, "% Clay" %>

script/db_maintenance/README

@@ -15,7 +15,7 @@ This script was motivated by the need to repair a database where the id numbers
 for new rows were allocated in the wrong range—to be specific, they were
 allocated starting at 99000000001 rather than starting at the number
 corresponding to the id number of the machine where the database resides.  (See
-https://pecan.gitbook.io/betydb-documentation/betydb-system-administration/distributed-betydb#primary-key-allocations
+https://pecanproject.github.io/bety-documentation/technical/distributed-instances-of-betydb.html
 for a list of BETYdb instances and their corresponding primary key allocations.)
 
 When id numbers have been mis-allocated, three things must be done to repair the

script/load.bety.sh

@@ -250,7 +250,7 @@ ID_RANGE=1000000000
 # before anything is done, check to make sure database exists
 if ! psql ${PG_OPT} ${PG_USER} -lqt | cut -d \| -f 1 | grep -w "^ *${DATABASE} *$" > /dev/null ; then
   echo "Database ${DATABASE} does not exist, please create it:"
-  echo "(see https://pecan.gitbooks.io/betydb-documentation/content/installing_betydb.html)"
+  echo "(see https://pecanproject.github.io/bety-documentation/technical/deploying-a-production-copy-of-the-betydb-web-application.html)"
   echo "  psql ${PG_OPT} ${PG_USER} -c \"CREATE ROLE ${OWNER} WITH LOGIN CREATEDB NOSUPERUSER NOCREATEROLE PASSWORD 'password'\""
   echo "  psql ${PG_OPT} ${PG_USER} -c \"CREATE DATABASE ${DATABASE} WITH OWNER ${OWNER}\""
   exit 1

spec/rails_helper.rb

@@ -11,7 +11,7 @@
   require 'capybara/rspec'
 rescue => e
   puts e.message
-  puts "Go to https://pecan.gitbooks.io/betydb-documentation/content/automated_tests.html for instructions on setting up the testing environment."
+  puts "Go to https://pecanproject.github.io/bety-documentation/technical/automated-tests.html for instructions on setting up the testing environment."
   exit
 end