Merge remote-tracking branch 'origin/release-1.13.0'

.dockerignore

@@ -0,0 +1,31 @@
+# See https://docs.docker.com/engine/reference/builder/#dockerignore-file for more about ignoring files.
+
+# Ignore git directory.
+/.git/
+
+# Ignore bundler config.
+/.bundle
+
+# Ignore all environment files (except templates).
+/.env*
+!/.env*.erb
+
+# Ignore all default key files.
+/config/master.key
+/config/credentials/*.key
+
+# Ignore all logfiles and tempfiles.
+/log/*
+/tmp/*
+!/log/.keep
+!/tmp/.keep
+
+# Ignore pidfiles, but keep the directory.
+/tmp/pids/*
+!/tmp/pids/.keep
+
+# Ignore storage (uploaded files in development and any SQLite databases).
+/storage/*
+!/storage/.keep
+/tmp/storage/*
+!/tmp/storage/.keep

CHANGELOG.md

@@ -1,3 +1,23 @@
+### 1.13.0
+**Species+**
+* Fix security issue
+* Remove .spp suffix from Hybrids
+* Add CITES RST download from the public interface
+* Add new Identification materials documents (csv and pdf)
+* Fix GA missing functions on develop and staging envs
+* Include non standard (EN, ES, FR) languages to autocomplete mview
+* Fix commission notes documents loading
+* Allow matches anywhere in trade permit number string, instead of just the start
+* Add Chinese common names
+* Add first draft of dockerizing the app
+
+**Trade Monitoring Tool**
+* Update csvs
+* Fix downloads when no appendix is submitted
+
+**Checklist**
+* Include EU(Regions) to the geo entity types
+
 ### 1.12.0
 * Allow intersessional decisions to be created without start events or documents
 

Dockerfile

@@ -0,0 +1,35 @@
+# Dockerfile
+FROM ruby:2.3.1
+
+# The ruby:2.3.1 image is ancient, based of debian jessie which no longer
+# receives active security updates. Therefore we must declare the debian
+# archive as a source instead.
+RUN rm /etc/apt/sources.list && \
+  echo "deb http://archive.debian.org/debian-security jessie/updates main" \
+    >> /etc/apt/sources.list.d/jessie.list && \
+  echo "deb http://archive.debian.org/debian jessie main" \
+    >> /etc/apt/sources.list.d/jessie.list \
+;
+
+# Rails and SAPI has some additional dependencies, e.g. rake requires a JS
+# runtime, so attempt to get these from apt, where possible
+RUN apt-get update && apt-get install -y --force-yes \
+  libsodium-dev libgmp3-dev libssl-dev \
+  libpq-dev postgresql-client \
+  nodejs \
+  texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra \
+;
+# NB: Postgres client from Debian is 9.4 - not sure if this is acceptable
+
+RUN mkdir /SAPI
+WORKDIR /SAPI
+
+COPY Gemfile /SAPI/Gemfile
+COPY Gemfile.lock /SAPI/Gemfile.lock
+RUN gem install bundler -v 1.17.3
+RUN bundle install
+
+COPY . /SAPI
+
+EXPOSE 3000
+CMD ["rails", "server", "-b", "0.0.0.0"]

Gemfile

@@ -116,7 +116,6 @@ group :development do
   gem 'jslint_on_rails'
   gem 'git_pretty_accept'
   gem 'rubocop', '~> 0.40.0', require: false
-  gem 'letter_opener'
   gem 'rbnacl', '>= 3.2', '< 5.0'
   gem 'rbnacl-libsodium'
   gem 'bcrypt_pbkdf', '>= 1.0', '< 2.0'

Gemfile.lock

@@ -265,8 +265,6 @@ GEM
       activesupport (>= 3.0.0)
     launchy (2.4.3)
       addressable (~> 2.3)
-    letter_opener (1.4.1)
-      launchy (~> 2.2)
     listen (0.7.2)
     lumberjack (1.0.2)
     mail (2.5.5)
@@ -573,7 +571,6 @@ DEPENDENCIES
   json_spec (= 1.1.5)
   kaminari
   launchy
-  letter_opener
   memcache-client
   nested-hstore
   nested_form (~> 0.3.2)

app/assets/javascripts/cites_trade/application.js

@@ -786,15 +786,12 @@ $(document).ready(function(){
       $.cookie('cites_trade.csv_separator', csv_separator)
       query += '&filters[csv_separator]=' + csv_separator;
 
-      // google analytics function only defined on production
-      if (typeof(ga) === 'function') {
-        ga('send', {
-          hitType: 'event',
-          eventCategory: 'Downloads: ' + report_type,
-          eventAction: 'Format: CSV',
-          eventLabel: csv_separator
-        });
-      }
+      ga('send', {
+        hitType: 'event',
+        eventCategory: 'Downloads: ' + report_type,
+        eventAction: 'Format: CSV',
+        eventLabel: csv_separator
+      });
       downloadResults( decodeURIComponent( query ) );
       return
     }

app/assets/javascripts/species/controllers/downloads_controller.js.coffee

@@ -1,7 +1,7 @@
 Species.DownloadsController = Ember.Controller.extend Species.Spinner,
   needs: [
     'downloadsForCmsListings', 
-    'downloadsForCitesListings', 'downloadsForCitesRestrictions',
+    'downloadsForCitesListings', 'downloadsForCitesRestrictions', 'downloadsForCitesProcesses',
     'downloadsForEuListings', 'downloadsForEuDecisions'
   ]
   downloadsPopupVisible: false
@@ -23,6 +23,9 @@ Species.DownloadsController = Ember.Controller.extend Species.Spinner,
   legislationIsCitesRestrictions: ( ->
     @get('citesLegislation') == 'restrictions'
   ).property('citesLegislation')
+  legislationIsCitesProcesses: ( ->
+    @get('citesLegislation') == 'processes'
+  ).property('citesLegislation')
   legislationIsEuListings: ( ->
     @get('euLegislation') == 'listings'
   ).property('euLegislation')

app/assets/javascripts/species/controllers/downloads_for_cites_listings_controller.js.coffee

@@ -25,7 +25,7 @@ Species.DownloadsForCitesListingsController = Ember.Controller.extend
         }
       ).filter((e) ->
         e.taxonConcepts.length > 0
-      )      
+      )
     else
       @get('higherTaxaController.contentByRank')
   ).property('higherTaxaController.contentByRank.@each', 'taxonConceptQuery')
@@ -103,4 +103,4 @@ Species.DownloadsForCitesListingsController = Ember.Controller.extend
       @set('selectedTaxonConcepts', [])
 
     deleteGeoEntitySelection: (context) ->
-      @get('selectedGeoEntities').removeObject(context)
+      @get('selectedGeoEntities').removeObject(context)

app/assets/javascripts/species/controllers/downloads_for_cites_processes_controller.js.coffee

@@ -0,0 +1,123 @@
+Species.DownloadsForCitesProcessesController = Ember.Controller.extend
+  designation: 'cites'
+
+  needs: ['geoEntities','higherTaxaCitesEu', 'downloads']
+
+  higherTaxaController: ( ->
+    @get('controllers.higherTaxaCitesEu')
+  ).property()
+
+  geoEntityQuery: null
+  taxonConceptQuery: null
+  selectedGeoEntities: []
+  selectedTaxonConcepts: []
+  timeScope: 'current'
+  timeScopeIsCurrent: ( ->
+    @get('timeScope') == 'current'
+  ).property('timeScope')
+  years: [1975..new Date().getFullYear()]
+  selectedYears: []
+  processType: 'Both'
+  documentTypeIsCitesSuspensions: ( ->
+    @get('documentType') == 'CitesSuspensions'
+  ).property('documentType')
+
+  autoCompleteTaxonConcepts: ( ->
+    if @get('taxonConceptQuery') && @get('taxonConceptQuery').length > 0
+      re = new RegExp("^"+@get('taxonConceptQuery'),"i")
+      @get('higherTaxaController.contentByRank')
+      .map((e) =>
+        {
+          rankName: e.rankName
+          taxonConcepts: e.taxonConcepts.filter((item) =>
+            re.test item.get('fullName')
+          )
+        }
+      ).filter((e) ->
+        e.taxonConcepts.length > 0
+      )
+    else
+      @get('higherTaxaController.contentByRank')
+  ).property('higherTaxaController.contentByRank.@each', 'taxonConceptQuery')
+
+  autoCompleteRegions: ( ->
+    if @get('geoEntityQuery') && @get('geoEntityQuery').length > 0
+      re = new RegExp("(^|\\(| )"+@get('geoEntityQuery'),"i")
+      @get('controllers.geoEntities.regions')
+        .filter (item, index, enumerable) =>
+          re.test item.get('name')
+    else
+      @get('controllers.geoEntities.regions')
+  ).property('controllers.geoEntities.regions.@each', 'geoEntityQuery')
+
+  autoCompleteCountries: ( ->
+    if @get('geoEntityQuery') && @get('geoEntityQuery').length > 0
+      re = new RegExp("(^|\\(| )"+@get('geoEntityQuery'),"i")
+      @get('controllers.geoEntities.countries')
+        .filter (item, index, enumerable) =>
+          re.test item.get('name')
+    else
+      @get('controllers.geoEntities.countries')
+  ).property('controllers.geoEntities.countries.@each', 'geoEntityQuery')
+
+  selectedGeoEntitiesIds: ( ->
+    @get('selectedGeoEntities').mapProperty('id')
+  ).property('selectedGeoEntities.@each')
+
+  selectedTaxonConceptsIds: ( ->
+    @get('selectedTaxonConcepts').mapProperty('id')
+  ).property('selectedTaxonConcepts.@each')
+
+  toParams: ( ->
+    {
+      data_type: 'Processes'
+      filters:
+        process_type: @get('processType')
+        designation: @get('designation')
+        geo_entities_ids: @get('selectedGeoEntitiesIds')
+        taxon_concepts_ids: @get('selectedTaxonConceptsIds')
+        set: @get('timeScope')
+        years: @get('selectedYears')
+        csv_separator: @get('controllers.downloads.csvSeparator')
+    }
+  ).property(
+    'selectedGeoEntitiesIds.@each', 'selectedTaxonConceptsIds.@each',
+    'timeScope', 'selectedYears.@each', 'processType', 'controllers.downloads.csvSeparator'
+  )
+
+  downloadUrl: ( ->
+    '/species/exports/download?' + $.param(@get('toParams'))
+  ).property('toParams')
+
+  actions:
+    startDownload: () ->
+      @set('downloadInProgress', true)
+      @set('downloadMessage', 'Downloading...')
+      $.ajax({
+        type: 'GET'
+        dataType: 'json'
+        url: @get('downloadUrl')
+      }).done((data) =>
+        @set('downloadInProgress', false)
+        if data.total > 0
+          @set('downloadMessage', null)
+          ga('send', {
+            hitType: 'event',
+            eventCategory: 'Downloads: ' + @get('processType'),
+            eventAction: 'Format: CSV',
+            eventLabel: @get('controllers.downloads.csvSeparator')
+          })
+          window.location = @get('downloadUrl')
+          return
+        else
+          @set('downloadMessage', 'No results')
+      )
+
+    deleteTaxonConceptSelection: (context) ->
+      @set('selectedTaxonConcepts', [])
+
+    deleteGeoEntitySelection: (context) ->
+      @get('selectedGeoEntities').removeObject(context)
+
+    deleteYearSelection: (context) ->
+      @get('selectedYears').removeObject(Number(context))

app/assets/javascripts/species/controllers/elibrary_search_controller.js.coffee

@@ -33,7 +33,8 @@ Species.ElibrarySearchController = Ember.Controller.extend Species.Spinner,
     allDocumentTypes = @get('controllers.events.documentTypes')
       .concat @get('controllers.events.interSessionalDocumentTypes')
       .concat @get('controllers.events.identificationDocumentTypes')
-
+    if @get('isSignedIn')
+      allDocumentTypes = allDocumentTypes.concat(@get('controllers.events.interSessionalNonPublicDocumentTypes'))
     @set('selectedDocumentType', allDocumentTypes.findBy('id', filtersHash.document_type))
 
     general_subtype_type = @get_general_subtype_type(filtersHash)
@@ -71,10 +72,10 @@ Species.ElibrarySearchController = Ember.Controller.extend Species.Spinner,
       general_subtype: isGeneralSubType
     }
 
-  getDocTypeParam: -> 
+  getDocTypeParam: ->
     id = @get('selectedDocumentType.id')
 
-    if id != '__all__' then id else null 
+    if id != '__all__' then id else null
 
   filteredDocumentTypes: ( ->
     if @get('selectedEventType')