Merge branch 'release-0.9.0'

Author: agnessa

CHANGELOG.md

@@ -1,3 +1,11 @@
+### 0.9.0 (2014-12-16)
+**Species+ Admin:**
+* nomenclature management (temporarily disabled)
+* changes to user roles (adding API users)
+
+**Species+:**
+* fixes to CITES Suspensions downloads and wording of sources
+
 ### 0.8.11 (2014-11-25)
 **Species+ Admin:**
 * fix for phantom opinions

Gemfile

@@ -22,6 +22,7 @@ gem 'devise'
 gem 'cancan'
 gem 'ahoy_matey'
 gem 'gon'
+gem 'wicked'
 
 gem 'sidekiq'
 gem 'sidekiq-status'
@@ -35,8 +36,8 @@ gem 'jquery-mousewheel-rails'
 gem 'jquery-cookie-rails'
 gem 'bootstrap-sass', '~> 2.3.1.0'
 gem 'kaminari'
-gem 'select2-rails'
-gem 'nested_form', '~> 0.3.1'
+gem 'select2-rails', '~> 3.5.7'
+gem 'nested_form', '~> 0.3.2'
 gem 'acts-as-taggable-on', '~> 2.3.1'
 gem 'carrierwave'
 
@@ -107,13 +108,16 @@ group :test, :development do
   gem "json_spec"
   gem "database_cleaner", ">=1.2.0"
   gem "timecop"
+  gem "launchy"
+  gem 'byebug'
 end
 
 group :test do
   gem "codeclimate-test-reporter", require: nil
   gem "factory_girl_rails", "~> 4.0"
   gem 'simplecov', :require => false
   gem 'coveralls', :require => false
+  gem 'capybara'
 end
 
 gem 'rake', '~> 10.0.3'

Gemfile.lock

@@ -84,6 +84,9 @@ GEM
       capistrano (>= 2.5)
     browser (0.6.0)
     builder (3.0.4)
+    byebug (3.2.0)
+      columnize (~> 0.8)
+      debugger-linecache (~> 1.2)
     cancan (1.6.10)
     capistrano (2.15.4)
       highline
@@ -95,6 +98,12 @@ GEM
       capistrano (>= 1.0.0)
     capistrano-log_with_awesome (0.0.2)
       capistrano (>= 2.5.14)
+    capybara (2.4.4)
+      mime-types (>= 1.16)
+      nokogiri (>= 1.3.3)
+      rack (>= 1.0.0)
+      rack-test (>= 0.5.4)
+      xpath (~> 2.0)
     carrierwave (0.10.0)
       activemodel (>= 3.2.0)
       activesupport (>= 3.2.0)
@@ -119,6 +128,7 @@ GEM
       execjs
     coffee-script-source (1.4.0)
     colorize (0.5.8)
+    columnize (0.8.9)
     compass (0.12.2)
       chunky_png (~> 1.2)
       fssm (>= 0.2.7)
@@ -136,6 +146,7 @@ GEM
       rails (>= 3.0.0)
     database_cleaner (1.2.0)
     debug_inspector (0.0.2)
+    debugger-linecache (1.2.0)
     devise (3.2.4)
       bcrypt (~> 3.0)
       orm_adapter (~> 0.1)
@@ -224,6 +235,8 @@ GEM
     kaminari (0.14.1)
       actionpack (>= 3.0.0)
       activesupport (>= 3.0.0)
+    launchy (2.4.3)
+      addressable (~> 2.3)
     listen (0.7.2)
     lumberjack (1.0.2)
     mail (2.5.4)
@@ -240,18 +253,18 @@ GEM
       activerecord
       activerecord-postgres-hstore
       activesupport
-    nested_form (0.3.1)
+    nested_form (0.3.2)
     net-scp (1.1.1)
       net-ssh (>= 2.6.5)
     net-sftp (2.1.2)
       net-ssh (>= 2.6.5)
     net-ssh (2.6.7)
     net-ssh-gateway (1.2.0)
       net-ssh (>= 2.6.5)
-    netrc (0.7.7)
-    nokogiri (1.6.3.1)
-      mini_portile (= 0.6.0)
-    oj (2.1.4)
+    netrc (0.7.9)
+    nokogiri (1.6.5)
+      mini_portile (~> 0.6.0)
+    oj (2.11.1)
     orm_adapter (0.5.0)
     pg (0.17.1)
     pg-hstore (1.2.0)
@@ -330,7 +343,7 @@ GEM
       railties (~> 3.2.0)
       sass (>= 3.1.10)
       tilt (~> 1.3)
-    select2-rails (3.2.1)
+    select2-rails (3.5.7)
       thor (~> 0.14)
     sentient_user (0.3.3)
       railties (>= 3.1)
@@ -395,6 +408,10 @@ GEM
     whenever (0.8.4)
       activesupport (>= 2.3.4)
       chronic (>= 0.6.3)
+    wicked (1.0.3)
+      rails (>= 3.0.7)
+    xpath (2.0.0)
+      nokogiri (~> 1.3)
     yajl-ruby (1.1.0)
 
 PLATFORMS
@@ -410,10 +427,12 @@ DEPENDENCIES
   binding_of_caller (>= 0.7.2)
   bootstrap-sass (~> 2.3.1.0)
   brightbox (>= 2.3.9)
+  byebug
   cancan
   capistrano
   capistrano-ext
   capistrano-slack!
+  capybara
   carrierwave
   clerk
   codeclimate-test-reporter
@@ -443,9 +462,10 @@ DEPENDENCIES
   jslint_on_rails
   json_spec
   kaminari
+  launchy
   memcache-client
   nested-hstore
-  nested_form (~> 0.3.1)
+  nested_form (~> 0.3.2)
   nokogiri
   oj
   pg
@@ -461,7 +481,7 @@ DEPENDENCIES
   rspec-rails
   rvm-capistrano
   sass-rails (~> 3.2.3)
-  select2-rails
+  select2-rails (~> 3.5.7)
   sextant
   sidekiq
   sidekiq-status
@@ -477,4 +497,5 @@ DEPENDENCIES
   underscore-rails
   webrick (= 1.3.1)
   whenever
+  wicked
   yajl-ruby

app/assets/javascripts/admin/nomenclature_changes.js.coffee

@@ -0,0 +1,161 @@
+$(document).ready ->
+  defaultTaxonSelect2Options = {
+    placeholder: 'Start typing scientific name'
+    width: '300px'
+    minimumInputLength: 3
+    quietMillis: 500
+    allowClear: true
+    initSelection: (element, callback) =>
+      id = $(element).val()
+      if (id != null && id != '')
+        callback({id: id, text: $(element).attr('data-name') + ' ' + $(element).attr('data-name-status')})
+
+    ajax:
+      url: '/admin/taxon_concepts/autocomplete'
+      dataType: 'json'
+      data: (query, page) ->
+        search_params:
+          scientific_name: query
+          name_status: this.data('name-status-filter')
+          taxonomy:
+            id: this.data('taxonomy-id')
+        per_page: 25
+        page: 1
+      results: (data, page) => # parse the results into the format expected by Select2.
+        formatted_taxon_concepts = data.map (tc) =>
+          id: tc.id
+          text: tc.full_name + ' ' + tc.name_status
+        results: formatted_taxon_concepts
+  }
+  $('.taxon-concept').select2(defaultTaxonSelect2Options)
+  $('.taxon-concept').on('change', (event) ->
+    return false unless event.val
+    $.when($.ajax( '/admin/taxon_concepts/' + event.val + '.json' ) ).then(( data, textStatus, jqXHR ) =>
+      $(this).attr('data-name', data.full_name)
+      $(this).attr('data-name-status', data.name_status)
+      if $(this).hasClass('status-change')
+        # reload the name status dropdown based on selection
+        statusDropdown = $(this).closest('.fields').find('select')
+        statusFrom = data.name_status
+        $(statusDropdown).find('option').attr('disabled', true)
+        statusMap =
+          'A': ['S']
+          'N': ['A', 'S']
+          'S': ['A']
+          'T': ['A', 'S']
+        $(statusDropdown).find('option[value=' + statusFrom + ']').removeAttr('selected')
+        defaultStatus = statusMap[statusFrom][0]
+        $(statusDropdown).find('option[value=' + defaultStatus + ']').attr('selected', true)
+        $.each(statusMap[statusFrom], (i, status) ->
+          $(statusDropdown).find('option[value=' + status + ']').removeAttr('disabled')
+        )
+    )
+    if $(this).hasClass('clear-others')
+      # reset selection in other taxon concept select2 instances
+      $('input.taxon-concept').not($(this)).each((i, ac) ->
+        $(ac).select2('val', '')
+        $(ac).removeAttr('data-name')
+        $(ac).removeAttr('data-name-status')
+      )
+  )
+
+  $(document).on('nested:fieldAdded', (event) ->
+    # this field was just inserted into your form
+    field = event.field
+    # it's a jQuery object already
+    taxonField = field.find('.taxon-concept')
+    # and activate select2
+    taxonField.select2(defaultTaxonSelect2Options)
+  )
+
+  simpleTaxonSelect2Options = {
+    placeholder: 'Start typing scientific name'
+    width: '200px'
+  }
+  $('.simple-taxon-concept').select2(simpleTaxonSelect2Options)
+  .on('select2-removed', (event) ->
+    $(this).closest('.controls').find('.select-all-checkbox').prop('checked', false)
+
+    $('.species-checkbox:contains('+event.choice.text+')')
+    .find('.select-partial-checkbox').prop('checked', false)
+  )
+
+  $('.select-all-checkbox').click (e) ->
+      checkboxElement = $(e.target)
+      selectElement = checkboxElement.parent().find('select')
+      if checkboxElement.is(':checked')
+        selectElement.find('option').prop("selected","selected")
+      else
+        selectElement.find('option').removeAttr("selected")
+      selectElement.trigger("change")
+
+  $('.select-partial-checkbox').click (e) ->
+      checkboxElement = $(e.target)
+      species = $(checkboxElement).parent().find('span').text()
+      selectElement = checkboxElement.parent().parent().find('select')
+      if checkboxElement.is(':checked')
+        selectElement.find('option:contains('+species+')').prop("selected","selected")
+      else
+        selectElement.find('option:contains('+species+')').removeAttr("selected")
+      selectElement.trigger("change")
+
+  $('form').on('click', '.output-radio', (e) ->
+    value = $(this).val()
+    switch value
+      when "New taxon"
+        NewTaxonForm(this)
+      when "Existing taxon"
+        ExistingTaxonForm(this)
+      when "Existing subspecies"
+        UpgradedTaxonForm(this)
+  )
+
+  HideInputTaxon = (obj) ->
+    input_taxon = $(obj).closest('.fields').find('.input-taxon')
+    input_taxon.select2('data',null)
+    input_taxon.hide()
+    input_taxon.closest('.control-group').find('label').hide()
+
+  ShowInputTaxon = (obj) ->
+    input_taxon = $(obj).closest('.fields').find('.input-taxon')
+    input_taxon.show()
+    input_taxon.closest('.control-group').find('label').show()
+
+  HideUpgradeInfo = (obj) ->
+    upgrade_info = $(obj).closest('.fields').find('.upgrade-info')
+    upgrade_info.first().hide()
+    upgrade_info.find('input').prop("value", '')
+    $(obj).closest('.fields').find('.parent-taxon').select2('data',null)
+
+  NewTaxonForm = (obj) ->
+    HideInputTaxon(obj)
+    $(obj).closest('.fields').find('.upgrade-info').first().show()
+
+  ExistingTaxonForm = (obj) ->
+    ShowInputTaxon(obj)
+    HideUpgradeInfo(obj)
+
+  UpgradedTaxonForm = (obj) ->
+    ShowInputTaxon(obj)
+    $(obj).closest('.fields').find('.upgrade-info').first().show()
+
+  DefaultExistingTaxon = (obj) ->
+    $(obj).find('.output-radio[value="Existing taxon"]').attr("checked","checked")
+    ExistingTaxonForm(obj)
+
+  OutputsDefaultConfiguration = ->
+    $('.fields').each (index) ->
+      taxon_concept = $(this).find('input.input-taxon')
+      parent = $(this).find('input.parent-taxon')
+
+      if typeof taxon_concept.attr("data-name") == 'undefined'
+        $(this).find('.output-radio[value="New taxon"]').attr("checked","checked")
+        NewTaxonForm(this)
+      else if typeof parent.attr("data-name") == 'undefined'
+        $(this).find('.output-radio[value="Existing taxon"]').attr("checked","checked")
+        ExistingTaxonForm(this)
+      else
+        $(this).find('.output-radio[value="Existing subspecies"]').attr("checked","checked")
+        UpgradedTaxonForm(this)
+
+  OutputsDefaultConfiguration()

app/assets/javascripts/admin/tag.js.coffee

@@ -16,4 +16,3 @@
 //= require bootstrap-dropdown
 //= require bootstrap-button
 //= require select2
-//= require_tree ./application

app/assets/javascripts/application.js

@@ -35,7 +35,7 @@
             {{#if decision.subspecies_info}}
               {{{decision.subspecies_info}}}<br />
             {{/if}}
-            {{decision.term.name}} {{decision.source.name}} <br />
+            {{decision.term.name}} {{#if decision.source.code}}{{decision.source.code}} - {{decision.source.name}}{{/if}} <br />
             {{{decision.notes}}}
           </td>
           <td class="last">
@@ -86,7 +86,7 @@
                 {{#if decision.subspecies_info}}
                   {{{decision.subspecies_info}}}<br />
                 {{/if}}
-                {{decision.term.name}} {{decision.source.name}} <br />
+                {{decision.term.name}} {{#if decision.source.code}}{{decision.source.code}} - {{decision.source.name}}{{/if}} <br />
                 {{{decision.notes}}}
               </td>
               <td class="last">