diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000000..bb56dafc18 --- /dev/null +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index bc8c165135..451d38915a 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000000..c0dbdd9db1 --- /dev/null +++ b/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"] diff --git a/Gemfile b/Gemfile index 8624050c80..c3520a1bca 100644 --- a/Gemfile +++ b/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' diff --git a/Gemfile.lock b/Gemfile.lock index 050cc86168..1cc78f2727 100644 --- a/Gemfile.lock +++ b/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) diff --git a/app/assets/javascripts/cites_trade/application.js b/app/assets/javascripts/cites_trade/application.js index 9e7336df88..e722056765 100644 --- a/app/assets/javascripts/cites_trade/application.js +++ b/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 } diff --git a/app/assets/javascripts/species/controllers/downloads_controller.js.coffee b/app/assets/javascripts/species/controllers/downloads_controller.js.coffee index 7682ecd1ee..f488c2dfe8 100644 --- a/app/assets/javascripts/species/controllers/downloads_controller.js.coffee +++ b/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') diff --git a/app/assets/javascripts/species/controllers/downloads_for_cites_listings_controller.js.coffee b/app/assets/javascripts/species/controllers/downloads_for_cites_listings_controller.js.coffee index 120ea591d8..5f8f9a993e 100644 --- a/app/assets/javascripts/species/controllers/downloads_for_cites_listings_controller.js.coffee +++ b/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) \ No newline at end of file + @get('selectedGeoEntities').removeObject(context) diff --git a/app/assets/javascripts/species/controllers/downloads_for_cites_processes_controller.js.coffee b/app/assets/javascripts/species/controllers/downloads_for_cites_processes_controller.js.coffee new file mode 100644 index 0000000000..8012dcbd8a --- /dev/null +++ b/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)) diff --git a/app/assets/javascripts/species/controllers/elibrary_search_controller.js.coffee b/app/assets/javascripts/species/controllers/elibrary_search_controller.js.coffee index 0ebb2e3508..846b0ab3dd 100644 --- a/app/assets/javascripts/species/controllers/elibrary_search_controller.js.coffee +++ b/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') diff --git a/app/assets/javascripts/species/templates/downloads_for_cites.handlebars b/app/assets/javascripts/species/templates/downloads_for_cites.handlebars index 14df63ce5d..b30c018532 100644 --- a/app/assets/javascripts/species/templates/downloads_for_cites.handlebars +++ b/app/assets/javascripts/species/templates/downloads_for_cites.handlebars @@ -4,11 +4,16 @@ LISTINGS {{/view}} -
  • +
  • {{#view Species.ToggleButton option="restrictions" valueBinding="controller.citesLegislation"}} QUOTAS/SUSPENSIONS {{/view}}
    • +
  • + {{#view Species.ToggleButton option="processes" valueBinding="controller.citesLegislation"}} + Processes + {{/view}} +
    • {{#view Species.DownloadsForLegislation isVisibleBinding="controller.legislationIsCitesListings" @@ -136,3 +141,84 @@ {{/view}} +{{#view Species.DownloadsForLegislation + isVisibleBinding="controller.legislationIsCitesProcesses" + controllerBinding="controllers.downloadsForCitesProcesses" +}} +
    +
    +
    + +
    +
    + +
    +
    + +
    +
    +
    +
    +
    + +
    +
    + {{#if timeScopeIsCurrent}} + Only current data has
    been selected. + {{else}} + {{#unless documentTypeIsCitesSuspensions}} +
    + {{view Species.YearSearchButton selectedYearsBinding="controller.selectedYears"}} + {{view Species.YearSearchDropdown controllerBinding="controller"}} +
    + {{/unless}} + {{/if}} +
    +
    +
    +
    +
    + {{view Species.HigherTaxaSearchButton controllerBinding="controller"}} + {{view Species.HigherTaxaSearchDropdown controllerBinding="controller"}} +
    +
    +
    +
    + {{view Species.GeoEntitiesSearchButton + selectedGeoEntitiesBinding="controller.selectedGeoEntities" + loadedBinding="controller.loaded" + }} + {{view Species.GeoEntitiesSearchDropdown controllerBinding="controller"}} +
    +
    +
    +
    + {{view Species.StartDownloadButton controllerBinding="controller"}} +
    + {{#if controller.downloadInProgress}} + + {{/if}} + {{controller.downloadMessage}} +
    +
    +{{/view}} diff --git a/app/assets/javascripts/species/templates/taxon_concept.handlebars b/app/assets/javascripts/species/templates/taxon_concept.handlebars index e403f38597..47d8e14822 100644 --- a/app/assets/javascripts/species/templates/taxon_concept.handlebars +++ b/app/assets/javascripts/species/templates/taxon_concept.handlebars @@ -8,7 +8,7 @@ {{/if}}

    {{fullName}}

    -

    {{authorYear}}

    +

    {{authorYear}}

    diff --git a/app/views/layouts/species.html.erb b/app/views/layouts/species.html.erb index 51f969d627..c78b690c8a 100644 --- a/app/views/layouts/species.html.erb +++ b/app/views/layouts/species.html.erb @@ -33,6 +33,12 @@ <%= render "species/hotjar" %> + <% else %> + <% end %> diff --git a/config/database.yml.sample b/config/database.yml.sample index 9ccf47c5f8..64521c8416 100644 --- a/config/database.yml.sample +++ b/config/database.yml.sample @@ -1,47 +1,29 @@ -# SQLite version 3.x -# gem install sqlite3 -# -# Ensure the SQLite 3 gem is defined in your Gemfile -# gem 'sqlite3' -development: + +default: &default + host: <%= ENV.fetch("SAPI_DATABASE_HOST", 'localhost') %> adapter: postgresql + encoding: unicode + # For details on connection pooling, see Rails configuration guide + # https://guides.rubyonrails.org/configuring.html#database-pooling + pool: <%= ENV.fetch("SAPI_RAILS_MAX_THREADS") { 5 } %> + username: <%= ENV.fetch("SAPI_DATABASE_USERNAME", 'postgres') %> + port: <%= ENV.fetch("SAPI_DATABASE_PORT", 5432) %> + +development: + <<: *default database: sapi_development - pool: 5 - username: postgres - password: timeout: 5000 - port: 5432 - host: localhost -# Warning: The database defined as "test" will be erased and -# re-generated from your development database when you run "rake". -# Do not set this db to the same as development or production. test: - adapter: postgresql + <<: *default database: sapi_test - pool: 5 - username: postgres - password: timeout: 5000 - port: 5432 - host: localhost staging: - adapter: postgresql + <<: *default database: sapi_development - pool: 10 - username: postgres - password: - host: localhost port: 5432 - template: template0 production: - adapter: postgresql + <<: *default database: sapi_development - pool: 10 - username: postgres - password: - host: localhost - port: 5432 - template: template0 diff --git a/config/environments/development.rb b/config/environments/development.rb index 143771cc18..cb760648ed 100644 --- a/config/environments/development.rb +++ b/config/environments/development.rb @@ -18,12 +18,15 @@ config.action_mailer.raise_delivery_errors = false config.action_mailer.default_url_options = { - host: Rails.application.secrets.mailer['host'] + host: Rails.application.secrets.mailer['host'] || 'http://localhost:3000' } ActionMailer::Base.default from: Rails.application.secrets.mailer['from'] - config.action_mailer.delivery_method = :letter_opener + # config.action_mailer.delivery_method = :letter_opener + # Mail server configuration. Development use mailcatcher. + config.action_mailer.delivery_method = :smtp + config.action_mailer.smtp_settings = { address: Rails.application.secrets.mailer['address'], port: 1025 } # Print deprecation notices to the Rails logger config.active_support.deprecation = :log diff --git a/config/secrets.yml b/config/secrets.yml index ccaf687f77..9598e19f7a 100644 --- a/config/secrets.yml +++ b/config/secrets.yml @@ -9,7 +9,7 @@ common: &defaults from: <%= ENV["MAILER_USERNAME"] %> redis: namespace: 'SAPI' - url: 'redis://127.0.0.1:6379/1' + url: <%= ENV["SAPI_SIDEKIQ_REDIS_URL"] || 'redis://127.0.0.1:6379/1' %> aws: bucket_name: <%= ENV["AWS_BUCKET_NAME"] %> access_key_id: <%= ENV["AWS_ACCESS_KEY_ID"] %> diff --git a/db/helpers/000_helpers.sql b/db/helpers/000_helpers.sql index aeefbc3ec2..5393152a89 100644 --- a/db/helpers/000_helpers.sql +++ b/db/helpers/000_helpers.sql @@ -18,18 +18,21 @@ CREATE OR REPLACE FUNCTION squish_null(TEXT) RETURNS TEXT COMMENT ON FUNCTION squish_null(TEXT) IS 'Squishes whitespace characters in a string and returns null for empty string'; -CREATE OR REPLACE FUNCTION full_name_with_spp(rank_name VARCHAR(255), full_name VARCHAR(255)) RETURNS VARCHAR(255) +-- This function previously had a different signature - ensure that the old version is gone +DROP FUNCTION IF EXISTS full_name_with_spp(rank_name VARCHAR(255), full_name VARCHAR(255)); + +CREATE OR REPLACE FUNCTION full_name_with_spp(rank_name VARCHAR(255), full_name VARCHAR(255), name_status CHAR(1)) RETURNS VARCHAR(255) LANGUAGE sql IMMUTABLE AS $$ SELECT CASE - WHEN $1 IN ('ORDER', 'FAMILY', 'SUBFAMILY', 'GENUS') + WHEN $1 IN ('ORDER', 'FAMILY', 'SUBFAMILY', 'GENUS') AND $3 != 'H' THEN $2 || ' spp.' ELSE $2 END; $$; -COMMENT ON FUNCTION full_name_with_spp(rank_name VARCHAR(255), full_name VARCHAR(255)) IS - 'Returns full name with ssp where applicable depending on rank.'; +COMMENT ON FUNCTION full_name_with_spp(rank_name VARCHAR(255), full_name VARCHAR(255), name_status CHAR(1)) IS + 'Returns full name with ssp where applicable depending on rank. This is not applied for higher than species level hybrids'; DROP FUNCTION IF EXISTS ancestor_listing_auto_note(rank_name VARCHAR(255), full_name VARCHAR(255), change_type_name VARCHAR(255)); @@ -54,7 +57,7 @@ RETURNS TEXT change_types.display_name_en, change_types.name ) || '' '' || - full_name_with_spp(ranks.name, ''' || taxon_concept.full_name || ''') + full_name_with_spp(ranks.name, ''' || taxon_concept.full_name || ''', ''' || taxon_concept.name_status || ''') FROM ranks, change_types WHERE ranks.id = ' || taxon_concept.rank_id || ' AND change_types.id = ' || listing_change.change_type_id @@ -186,7 +189,7 @@ CREATE OR REPLACE FUNCTION create_trade_sandbox_view( CASE WHEN aru.point_of_view = ''E'' THEN trading_partner - ELSE geo_entities.iso_code2 + ELSE geo_entities.iso_code2 END AS importer, taxon_concepts.full_name AS accepted_taxon_name, taxon_concepts.data->''rank_name'' AS rank, diff --git a/db/migrate/20230803181442_remove_language_restrictions_from_autocomplete_view.rb b/db/migrate/20230803181442_remove_language_restrictions_from_autocomplete_view.rb new file mode 100644 index 0000000000..192839d594 --- /dev/null +++ b/db/migrate/20230803181442_remove_language_restrictions_from_autocomplete_view.rb @@ -0,0 +1,15 @@ +class RemoveLanguageRestrictionsFromAutocompleteView < ActiveRecord::Migration + def up + execute "DROP VIEW IF EXISTS auto_complete_taxon_concepts_view" + execute "CREATE VIEW auto_complete_taxon_concepts_view AS #{view_sql('20230803181442', 'auto_complete_taxon_concepts_view')}" + execute File.read(File.expand_path('../../mviews/011_rebuild_auto_complete_taxon_concepts_mview.sql', __FILE__)) + execute "SELECT * FROM rebuild_auto_complete_taxon_concepts_mview()" + end + + def down + execute "DROP VIEW IF EXISTS auto_complete_taxon_concepts_view" + execute "CREATE VIEW auto_complete_taxon_concepts_view AS #{view_sql('20220808123526', 'auto_complete_taxon_concepts_view')}" + execute File.read(File.expand_path('../../mviews/011_rebuild_auto_complete_taxon_concepts_mview.sql', __FILE__)) + execute "SELECT * FROM rebuild_auto_complete_taxon_concepts_mview()" + end +end diff --git a/db/migrate/20230915113624_add_trigram_index_to_trade_permit_numbers.rb b/db/migrate/20230915113624_add_trigram_index_to_trade_permit_numbers.rb new file mode 100644 index 0000000000..72876244d5 --- /dev/null +++ b/db/migrate/20230915113624_add_trigram_index_to_trade_permit_numbers.rb @@ -0,0 +1,20 @@ +class AddTrigramIndexToTradePermitNumbers < ActiveRecord::Migration + def up + # Index to optimise LIKE queries + if Rails.env.staging? or Rails.env.production? + puts "Please add extension by hand: CREATE EXTENSION pg_trgm" + else + execute "CREATE EXTENSION IF NOT EXISTS pg_trgm" + end + execute 'CREATE INDEX trade_permits_number_trigm_idx ON trade_permits USING gin (upper(number) gin_trgm_ops)' + end + + def down + execute 'DROP INDEX trade_permits_number_trigm_idx' + if Rails.env.staging? or Rails.env.production? + puts "Please drop extension by hand: DROP EXTENSION pg_trgm" + else + execute "DROP EXTENSION pg_trgm" + end + end +end diff --git a/db/mviews/007a_rebuild_cites_species_listing_mview.sql b/db/mviews/007a_rebuild_cites_species_listing_mview.sql index 207c5e76f2..f3dde8cc90 100644 --- a/db/mviews/007a_rebuild_cites_species_listing_mview.sql +++ b/db/mviews/007a_rebuild_cites_species_listing_mview.sql @@ -48,7 +48,8 @@ SELECT ARRAY_AGG( DISTINCT full_name_with_spp( COALESCE(inclusion_taxon_concepts_mview.rank_name, original_taxon_concepts_mview.rank_name), - COALESCE(inclusion_taxon_concepts_mview.full_name, original_taxon_concepts_mview.full_name) + COALESCE(inclusion_taxon_concepts_mview.full_name, original_taxon_concepts_mview.full_name), + COALESCE(inclusion_taxon_concepts_mview.name_status, original_taxon_concepts_mview.name_status) ) ), ',' diff --git a/db/mviews/007b_rebuild_eu_species_listing_mview.sql b/db/mviews/007b_rebuild_eu_species_listing_mview.sql index eb2602f3cc..6ac7516812 100644 --- a/db/mviews/007b_rebuild_eu_species_listing_mview.sql +++ b/db/mviews/007b_rebuild_eu_species_listing_mview.sql @@ -47,7 +47,8 @@ SELECT ARRAY_AGG( DISTINCT full_name_with_spp( COALESCE(inclusion_taxon_concepts_mview.rank_name, original_taxon_concepts_mview.rank_name), - COALESCE(inclusion_taxon_concepts_mview.full_name, original_taxon_concepts_mview.full_name) + COALESCE(inclusion_taxon_concepts_mview.full_name, original_taxon_concepts_mview.full_name), + COALESCE(inclusion_taxon_concepts_mview.name_status, original_taxon_concepts_mview.name_status) ) ), ',' diff --git a/db/mviews/007c_rebuild_cms_species_listing_mview.sql b/db/mviews/007c_rebuild_cms_species_listing_mview.sql index 7bd68727d9..3dbcdea8c3 100644 --- a/db/mviews/007c_rebuild_cms_species_listing_mview.sql +++ b/db/mviews/007c_rebuild_cms_species_listing_mview.sql @@ -27,7 +27,7 @@ SELECT taxon_concepts_mview.cms_listed, taxon_concepts_mview.cms_listing_original AS cms_listing_original, ARRAY_TO_STRING( - ARRAY_AGG(DISTINCT full_name_with_spp(original_taxon_concepts_mview.rank_name, original_taxon_concepts_mview.full_name)), + ARRAY_AGG(DISTINCT full_name_with_spp(original_taxon_concepts_mview.rank_name, original_taxon_concepts_mview.full_name, original_taxon_concepts_mview.name_status)), ',' ) AS original_taxon_concept_full_name_with_spp, ARRAY_TO_STRING( diff --git a/db/views/auto_complete_taxon_concepts_view/20230803181442.sql b/db/views/auto_complete_taxon_concepts_view/20230803181442.sql new file mode 100644 index 0000000000..65ba0f159b --- /dev/null +++ b/db/views/auto_complete_taxon_concepts_view/20230803181442.sql @@ -0,0 +1,199 @@ +WITH synonyms_segmented(taxon_concept_id, full_name, author_year, matched_taxon_concept_id, matched_name, matched_name_segment) AS ( + SELECT + atc.id, + atc.full_name, + atc.author_year, + tc.id, + tc.full_name, + UPPER(REGEXP_SPLIT_TO_TABLE(tc.full_name, ' ')) + FROM taxon_concepts tc + JOIN taxon_relationships tr + ON tr.other_taxon_concept_id = tc.id + JOIN taxon_relationship_types trt + ON trt.id = tr.taxon_relationship_type_id + AND trt.name = 'HAS_SYNONYM' + JOIN taxon_concepts atc + ON atc.id = tr.taxon_concept_id + WHERE tc.name_status = 'S' AND atc.name_status = 'A' +), scientific_names_segmented(taxon_concept_id, full_name, author_year, matched_taxon_concept_id, matched_name, matched_name_segment) AS ( + SELECT + id, + taxon_concepts.full_name, + taxon_concepts.author_year, + id, + taxon_concepts.full_name, + UPPER(REGEXP_SPLIT_TO_TABLE(full_name, ' ')) + FROM taxon_concepts +), unlisted_subspecies_segmented(taxon_concept_id, full_name, author_year, matched_taxon_concept_id, matched_name, matched_name_segment) AS ( + SELECT + parents.id, + parents.full_name, + parents.author_year, + taxon_concepts.id, + taxon_concepts.full_name, + UPPER(REGEXP_SPLIT_TO_TABLE(taxon_concepts.full_name, ' ')) + FROM taxon_concepts + JOIN ranks ON ranks.id = taxon_concepts.rank_id + AND ranks.name IN ('SUBSPECIES', 'VARIETY') + JOIN taxon_concepts parents + ON parents.id = taxon_concepts.parent_id + WHERE taxon_concepts.name_status NOT IN ('S', 'T', 'N') + AND parents.name_status = 'A' + + EXCEPT + + SELECT + parents.id, + parents.full_name, + parents.author_year, + taxon_concepts.id, + taxon_concepts.full_name, + UPPER(REGEXP_SPLIT_TO_TABLE(taxon_concepts.full_name, ' ')) + FROM taxon_concepts + JOIN ranks ON ranks.id = taxon_concepts.rank_id + AND ranks.name IN ('SUBSPECIES') -- VARIETY not here on purpose + JOIN taxon_concepts parents + ON parents.id = taxon_concepts.parent_id + JOIN taxonomies ON taxonomies.id = taxon_concepts.taxonomy_id + WHERE taxon_concepts.name_status NOT IN ('S', 'T', 'N') + AND parents.name_status = 'A' + AND CASE + WHEN taxonomies.name = 'CMS' + THEN (taxon_concepts.listing->'cms_historically_listed')::BOOLEAN + ELSE (taxon_concepts.listing->'cites_historically_listed')::BOOLEAN + OR (taxon_concepts.listing->'eu_historically_listed')::BOOLEAN + END +), taxon_common_names AS ( + SELECT + taxon_commons.*, + common_names.name + FROM taxon_commons + JOIN common_names + ON common_names.id = taxon_commons.common_name_id +), common_names_segmented(taxon_concept_id, full_name, author_year, matched_taxon_concept_id, matched_name, matched_name_segment) AS ( + SELECT + taxon_concept_id, + taxon_concepts.full_name, + taxon_concepts.author_year, + NULL::INT, + taxon_common_names.name, + UPPER(REGEXP_SPLIT_TO_TABLE(taxon_common_names.name, E'\\s|''')) + FROM taxon_common_names + JOIN taxon_concepts + ON taxon_common_names.taxon_concept_id = taxon_concepts.id +), taxon_common_names_dehyphenated AS ( + SELECT + taxon_concept_id, + taxon_concepts.full_name, + taxon_concepts.author_year, + NULL::INT, + taxon_common_names.name, + UPPER(REPLACE(taxon_common_names.name, '-', ' ')) + FROM taxon_common_names + JOIN taxon_concepts + ON taxon_common_names.taxon_concept_id = taxon_concepts.id + WHERE STRPOS(taxon_common_names.name, '-') > 0 +), common_names_segmented_dehyphenated AS ( + SELECT taxon_concept_id, full_name, author_year, matched_taxon_concept_id, matched_name, matched_name_segment + FROM common_names_segmented + UNION + SELECT taxon_concept_id, full_name, author_year, matched_taxon_concept_id, matched_name, REGEXP_SPLIT_TO_TABLE(matched_name_segment, E'-') + FROM common_names_segmented + WHERE STRPOS(matched_name_segment, '-') > 0 + UNION + SELECT * FROM taxon_common_names_dehyphenated +), all_names_segmented_cleaned AS ( + SELECT * FROM ( + SELECT taxon_concept_id, full_name, author_year, matched_taxon_concept_id, matched_name, + CASE + WHEN POSITION(matched_name_segment IN + UPPER(matched_name) + ) = 1 THEN UPPER(matched_name) + ELSE matched_name_segment + END, type_of_match + FROM ( + SELECT *, 'SELF' AS type_of_match + FROM scientific_names_segmented + UNION + SELECT *, 'SYNONYM' + FROM synonyms_segmented + UNION + SELECT *, 'SUBSPECIES' + FROM unlisted_subspecies_segmented + UNION + SELECT *, 'COMMON_NAME' + FROM common_names_segmented_dehyphenated + ) all_names_segmented + ) all_names_segmented_no_prefixes + WHERE LENGTH(matched_name_segment) >= 3 +), taxa_with_visibility_flags AS ( + SELECT taxon_concepts.id, + CASE + WHEN taxonomies.name = 'CITES_EU' THEN TRUE + ELSE FALSE + END AS taxonomy_is_cites_eu, + name_status, + ranks.name AS rank_name, + ranks.display_name_en AS rank_display_name_en, + ranks.display_name_es AS rank_display_name_es, + ranks.display_name_fr AS rank_display_name_fr, + ranks.taxonomic_position AS rank_order, + taxon_concepts.taxonomic_position, + CASE + WHEN + name_status = 'A' + AND ( + ranks.name != 'SUBSPECIES' + AND ranks.name != 'VARIETY' + OR taxonomies.name = 'CITES_EU' + AND ( + (listing->'cites_historically_listed')::BOOLEAN + OR (listing->'eu_historically_listed')::BOOLEAN + ) + OR taxonomies.name = 'CMS' + AND (listing->'cms_historically_listed')::BOOLEAN + ) + THEN TRUE + ELSE FALSE + END AS show_in_species_plus_ac, + CASE + WHEN + name_status = 'A' + AND ( + ranks.name != 'SUBSPECIES' + AND ranks.name != 'VARIETY' + OR (listing->'cites_show')::BOOLEAN + ) + THEN TRUE + ELSE FALSE + END AS show_in_checklist_ac, + CASE + WHEN + taxonomies.name = 'CITES_EU' + AND ARRAY['A', 'H', 'N']::VARCHAR[] && ARRAY[name_status] + THEN TRUE + ELSE FALSE + END AS show_in_trade_ac, + CASE + WHEN + taxonomies.name = 'CITES_EU' + AND ARRAY['A', 'H', 'N', 'T']::VARCHAR[] && ARRAY[name_status] + THEN TRUE + ELSE FALSE + END AS show_in_trade_internal_ac + FROM taxon_concepts + JOIN ranks ON ranks.id = rank_id + JOIN taxonomies ON taxonomies.id = taxon_concepts.taxonomy_id +) +SELECT + t1.*, + matched_name_segment AS name_for_matching, + matched_taxon_concept_id AS matched_id, + matched_name, + full_name, + author_year, + type_of_match +FROM taxa_with_visibility_flags t1 +JOIN all_names_segmented_cleaned t2 +ON t1.id = t2.taxon_concept_id +WHERE LENGTH(matched_name_segment) >= 3; diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000000..1e82790097 --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,93 @@ +# docker-compose.yml +version: '3.8' + +networks: + sapi: + driver: bridge + +services: + db: + container_name: sapi-db + image: postgres:10 + healthcheck: + test: ["CMD", "pg_isready", "-U", "postgres"] + timeout: 45s + interval: 10s + retries: 10 + volumes: + - 'pgdata:/var/lib/postgresql/data' + ports: + - "${SAPI_CONTAINER_DB_PORT:-5432}:5432" + networks: + - sapi + environment: + POSTGRES_HOST_AUTH_METHOD: "trust" + POSTGRES_DB: "sapi_development" + + rails: + container_name: sapi-rails + build: + context: ./ + dockerfile: Dockerfile + command: /bin/bash -l -c "rm -f ./tmp/pids/server.pid && bundle install && bundle exec rails s -p 3000 -b '0.0.0.0'" + volumes: + - '.:/SAPI' + - bundler_gems:/usr/local/bundle + ports: + - '${SAPI_CONTAINER_RAILS_PORT:-3000}:3000' + networks: + - sapi + stdin_open: true + tty: true + environment: + MAILER_ADDRESS: sapi-mailcatcher + SAPI_DATABASE_HOST: sapi-db + SAPI_SIDEKIQ_REDIS_URL: redis://sapi-redis:6379/0 + depends_on: + - redis + - db + - mailcatcher + + redis: + container_name: sapi-redis + image: redis:7.2.0 + ports: + - "${SAPI_CONTAINER_REDIS_PORT:-6379}:6379" + networks: + - sapi + command: redis-server --save 20 1 --loglevel warning + volumes: + - redis_data:/data + + sidekiq: + container_name: sapi-sidekiq + build: + context: . + dockerfile: Dockerfile + networks: + - sapi + depends_on: + - db + - redis + - mailcatcher + command: /bin/bash -l -c "bundle install && bundle exec sidekiq -C config/sidekiq.yml" + volumes: + - '.:/SAPI' + - bundler_gems:/usr/local/bundle + environment: + MAILER_ADDRESS: sapi-mailcatcher + SAPI_DATABASE_HOST: sapi-db + SAPI_SIDEKIQ_REDIS_URL: redis://sapi-redis:6379/0 + + mailcatcher: + container_name: sapi-mailcatcher + image: sj26/mailcatcher + ports: + - "${SAPI_CONTAINER_MAILCATCHER_PORT:-1080}:1080" + networks: + - sapi + +volumes: + pgdata: + bundler_gems: + redis_data: diff --git a/lib/files/chinese_common_names.csv b/lib/files/chinese_common_names.csv new file mode 100644 index 0000000000..5e48c8bb9f --- /dev/null +++ b/lib/files/chinese_common_names.csv @@ -0,0 +1,1765 @@ +ComName,LangShort,RecId,Rank,Designation,ReferenceID +叉角羚,ZHO,5062,SPECIES,CITES_EU, +旋角羚,ZHO,4464,SPECIES,CITES_EU, +印度野牛,ZHO,5874,SPECIES,CITES_EU, +野牦牛,ZHO,7471,SPECIES,CITES_EU, +柬埔寨野牛,ZHO,11180,SPECIES,CITES_EU, +西里伯斯水牛,ZHO,4425,SPECIES,CITES_EU, +民都洛水牛,ZHO,8124,SPECIES,CITES_EU, +夸氏水牛,ZHO,10958,SPECIES,CITES_EU, +捻角山羊,ZHO,3780,SPECIES,CITES_EU, +中华鬣羚,ZHO,3881,SPECIES,CITES_EU, +红鬣羚,ZHO,3939,SPECIES,CITES_EU, +苏门答腊鬣羚,ZHO,7979,SPECIES,CITES_EU, +喜马拉雅鬣羚,ZHO,10594,SPECIES,CITES_EU, +詹氏小羚羊,ZHO,4194,SPECIES,CITES_EU, +居氏羚,ZHO,3080,SPECIES,CITES_EU, +细角羚,ZHO,9611,SPECIES,CITES_EU, +大貂羚安哥拉亚种,ZHO,12301,SUBSPECIES,CITES_EU, +赤斑羚,ZHO,4344,SPECIES,CITES_EU, +长尾斑羚,ZHO,7159,SPECIES,CITES_EU, +喜马拉雅斑羚,ZHO,9378,SPECIES,CITES_EU, +中华斑羚,ZHO,6231,SPECIES,CITES_EU, +苍羚,ZHO,10002,SPECIES,CITES_EU, +弯角大羚羊,ZHO,11205,SPECIES,CITES_EU, +阿拉伯大羚羊,ZHO,4154,SPECIES,CITES_EU, +安纳托利亚绵盘羊,ZHO,33589,SPECIES,CITES_EU, +西藏盘羊,ZHO,98423,SPECIES,CITES_EU, +卡拉套盘羊,ZHO,30824,SPECIES,CITES_EU, +维氏绵盘羊,ZHO,4814,SPECIES,CITES_EU, +鬣羊,ZHO,3905,SPECIES,CITES_EU, +扭角羚,ZHO,3135,SPECIES,CITES_EU, +高加索羱羊,ZHO,67978,SPECIES,CITES_EU, +布氏小羚羊,ZHO,8418,SPECIES,CITES_EU, +骝毛小羚羊,ZHO,4497,SPECIES,CITES_EU, +奥氏小羚羊,ZHO,8002,SPECIES,CITES_EU, +黄背小羚羊,ZHO,10119,SPECIES,CITES_EU, +斑背小羚羊,ZHO,7092,SPECIES,CITES_EU, +白腿大羚羊指名亚种,ZHO,12162,SUBSPECIES,CITES_EU, +驴羚,ZHO,4050,SPECIES,CITES_EU, +阿尔泰盘羊,ZHO,7093,SPECIES,CITES_EU, +阿拉伯绵盘羊,ZHO,35596,SPECIES,CITES_EU, +塔吉克绵盘羊,ZHO,98436,SPECIES,CITES_EU, +加拿大盘羊,ZHO,3036,SPECIES,CITES_EU, +哈萨克盘羊,ZHO,98883,SPECIES,CITES_EU, +阿富汗绵盘羊,ZHO,98424,SPECIES,CITES_EU, +戈壁盘羊,ZHO,98884,SPECIES,CITES_EU, +雅布赖盘羊,ZHO,32866,SPECIES,CITES_EU, +天山盘羊,ZHO,98885,SPECIES,CITES_EU, +帕米尔盘羊,ZHO,98886,SPECIES,CITES_EU, +旁遮普绵盘羊,ZHO,98952,SPECIES,CITES_EU, +乌兹别克盘羊,ZHO,98887,SPECIES,CITES_EU, +褐麂羚,ZHO,101271,SPECIES,CITES_EU, +蓝小羚羊,ZHO,9997,SPECIES,CITES_EU, +岩羚羊阿布鲁左亚种,ZHO,12328,SUBSPECIES,CITES_EU, +北方高鼻羚羊,ZHO,9751,SPECIES,CITES_EU, +高鼻羚羊,ZHO,8765,SPECIES,CITES_EU, +印度羚,ZHO,4985,SPECIES,CITES_EU, +大蓝羚,ZHO,65574,SPECIES,CITES_EU, +印度水牛,ZHO,6811,SPECIES,CITES_EU, +野山羊,ZHO,65582,SUBSPECIES,CITES_EU, +北山羊,ZHO,65566,SPECIES,CITES_EU, +印度瞪羚,ZHO,65567,SPECIES,CITES_EU, +鹿羚,ZHO,5673,SPECIES,CITES_EU, +岩羊,ZHO,65584,SPECIES,CITES_EU, +四角羚,ZHO,9831,SPECIES,CITES_EU, +藏羚,ZHO,8117,SPECIES,CITES_EU, +安南锭角羚,ZHO,10395,SPECIES,CITES_EU, +原驼,ZHO,10716,SPECIES,CITES_EU, +鲟形目 ,ZHO,102,ORDER,CITES_EU, +卡岛豚鹿,ZHO,4889,SPECIES,CITES_EU, +巴岛豚鹿,ZHO,10380,SPECIES,CITES_EU, +豚鹿印支亚种,ZHO,12317,SUBSPECIES,CITES_EU, +南美泽鹿,ZHO,3625,SPECIES,CITES_EU, +马鹿克什米尔亚种,ZHO,12225,SUBSPECIES,CITES_EU, +黇鹿波斯亚种,ZHO,12218,SUBSPECIES,CITES_EU, +马鹿大夏亚种,ZHO,12260,SUBSPECIES,CITES_EU, +北普度鹿,ZHO,5742,SPECIES,CITES_EU, +豚鹿,ZHO,3218,SPECIES,CITES_EU, 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+玄参科,ZHO,12465,FAMILY,CITES_EU, +蕨苏铁科,ZHO,12540,FAMILY,CITES_EU, +紫杉科,ZHO,12484,FAMILY,CITES_EU, +瑞香科,ZHO,12544,FAMILY,CITES_EU, +水青树科,ZHO,12494,FAMILY,CITES_EU, +败酱科,ZHO,12468,FAMILY,CITES_EU, +葡萄科,ZHO,12549,FAMILY,CITES_EU, +百岁叶科,ZHO,12531,FAMILY,CITES_EU, +泽米科,ZHO,12502,FAMILY,CITES_EU, +姜科,ZHO,12525,FAMILY,CITES_EU, +蒺藜科,ZHO,12447,FAMILY,CITES_EU, diff --git a/lib/modules/downloads_cache.rb b/lib/modules/downloads_cache.rb index 0fb84e545d..158c1942bd 100644 --- a/lib/modules/downloads_cache.rb +++ b/lib/modules/downloads_cache.rb @@ -5,7 +5,7 @@ module DownloadsCache 'taxon_concepts_names', 'synonyms_and_trade_names', 'orphaned_taxon_concepts', 'taxon_concepts_distributions', 'common_names', 'species_reference_output', 'standard_reference_output', - 'documents' + 'documents', 'cites_processes' ] DOWNLOAD_DIRS = LISTINGS_DOWNLOAD_DIRS + [ 'quotas', 'cites_suspensions', 'eu_decisions', 'shipments', 'comptab', @@ -87,6 +87,10 @@ def self.clear_documents clear_dirs(['documents']) end + def self.clear_cites_processes + clear_dirs(['cites_processes']) + end + # cleared after destroy def self.clear_quotas clear_dirs(['quotas']) diff --git a/lib/modules/import/rst/importer.rb b/lib/modules/import/rst/importer.rb index b9f0980457..21e39283af 100644 --- a/lib/modules/import/rst/importer.rb +++ b/lib/modules/import/rst/importer.rb @@ -2,6 +2,9 @@ module Import::Rst::Importer class << self def import(data) + # Array of CitesRstProcesses in current import we can use to + # destroy records no longer being returned from the RST API. + active_ids = [] data.map do |item| taxon_concept = map_taxon_concept(item) unless taxon_concept @@ -29,7 +32,10 @@ def import(data) start_date: item['startDate'], document: "https://rst.cites.org/public/case-details/#{item['id']}" ) + active_ids << rst_process.id end + + destroy_invalid_rst_processes(active_ids) end private @@ -49,5 +55,16 @@ def map_event(item) Rails.logger.info "Event #{item['meeting']['name']} for case #{item['id']} not found" unless event event end + + def destroy_invalid_rst_processes(active_ids) + CitesRstProcess.where.not(id: active_ids).find_each do |rst_process| + case_id = rst_process.case_id + if rst_process.destroy + Rails.logger.info "RST process with case_id #{case_id} destroyed" + else + Rails.logger.info "RST process with case_id #{case_id} could not be destroyed" + end + end + end end end diff --git a/lib/modules/search_param_sanitiser.rb b/lib/modules/search_param_sanitiser.rb index 0faf45074c..2a04e21415 100644 --- a/lib/modules/search_param_sanitiser.rb +++ b/lib/modules/search_param_sanitiser.rb @@ -6,7 +6,7 @@ def sanitise_string(s) end def sanitise_upcase_string(s) - s && s.strip.upcase + s && s.strip.mb_chars.upcase end def sanitise_symbol(s, default = nil) diff --git a/lib/modules/trade/download_data_retriever.rb b/lib/modules/trade/download_data_retriever.rb index f18a149980..3e7e414e6f 100644 --- a/lib/modules/trade/download_data_retriever.rb +++ b/lib/modules/trade/download_data_retriever.rb @@ -48,13 +48,22 @@ def self.search_download(params) SQL when 'species' appendix = params[:appendix] - <<-SQL - SELECT #{ATTRIBUTES.join(',')} - FROM non_compliant_shipments_view - WHERE year = #{year} - AND taxon_concept_id IN (#{id}) - AND appendix = '#{appendix}' - SQL + if appendix.present? + <<-SQL + SELECT #{ATTRIBUTES.join(',')} + FROM non_compliant_shipments_view + WHERE year = #{year} + AND taxon_concept_id IN (#{id}) + AND appendix = '#{appendix}' + SQL + else + <<-SQL + SELECT #{ATTRIBUTES.join(',')} + FROM non_compliant_shipments_view + WHERE year = #{year} + AND taxon_concept_id IN (#{id}) + SQL + end when 'commodity' <<-SQL SELECT #{ATTRIBUTES.join(',')} diff --git a/lib/modules/trade/grouping/base.rb b/lib/modules/trade/grouping/base.rb index 9943824abb..d105b9147e 100644 --- a/lib/modules/trade/grouping/base.rb +++ b/lib/modules/trade/grouping/base.rb @@ -35,6 +35,20 @@ def json_by_attribute(data, opts={}) raise NotImplementedError end + def read_taxonomy_conversion + conversion = {} + taxonomy = CSV.read(TAXONOMIC_GROUPING, {headers: true}) + taxonomy.each do |csv| + conversion[csv['group']] ||= [] + data = { + taxon_name: csv['taxon_name'], + rank: csv['taxonomic_level'] + } + conversion[csv['group']] << data + end + conversion + end + protected def shipments_table @@ -80,20 +94,6 @@ def limit private - def read_taxonomy_conversion - conversion = {} - taxonomy = CSV.read(TAXONOMIC_GROUPING, {headers: true}) - taxonomy.each do |csv| - conversion[csv['group']] ||= [] - data = { - taxon_name: csv['taxon_name'], - rank: csv['taxonomic_level'] - } - conversion[csv['group']] << data - end - conversion - end - def sanitise_group(group) return nil unless group attributes[group.to_sym] diff --git a/lib/modules/trade/grouping/compliance.rb b/lib/modules/trade/grouping/compliance.rb index d2a1a581e3..5ecef93c4f 100644 --- a/lib/modules/trade/grouping/compliance.rb +++ b/lib/modules/trade/grouping/compliance.rb @@ -271,7 +271,11 @@ def only_importer_countries(importers, keys, year) end def group_query - columns = @attributes.compact.uniq.join(',') + columns = if @attributes + @attributes.compact.uniq.join(',') + else + attributes.values.join(',') + end <<-SQL SELECT #{columns}, COUNT(*) AS cnt, 100.0*COUNT(*)/(SUM(COUNT(*)) OVER (PARTITION BY year)) AS percent FROM non_compliant_shipments_view diff --git a/lib/tasks/db_migrate_plpgsql.rake b/lib/tasks/db_migrate_plpgsql.rake index 42d1ccae00..46685d251e 100644 --- a/lib/tasks/db_migrate_plpgsql.rake +++ b/lib/tasks/db_migrate_plpgsql.rake @@ -2,14 +2,20 @@ namespace :db do namespace :migrate do desc "Run custom sql scripts" task :sql => :environment do - ['helpers', 'mviews', 'plpgsql'].each do |dir| - files = Dir.glob(Rails.root.join("db/#{dir}/*.sql")) - files.sort.each do |file| - puts file - ActiveRecord::Base.connection.execute(File.read(file)) + ActiveRecord::Base.transaction do + connection = ActiveRecord::Base.connection + + ['helpers', 'mviews', 'plpgsql'].each do |dir| + files = Dir.glob(Rails.root.join("db/#{dir}/*.sql")) + + files.sort.each do |file| + puts "Executing #{file}" + connection.execute(File.read(file)) + end end end end + desc "Rebuild all computed values" task :rebuild => :migrate do Sapi.rebuild @@ -23,9 +29,11 @@ namespace :db do Sapi::create_indexes end end + task :migrate do Rake::Task['db:migrate:sql'].invoke end + desc "Drop sandboxes in progress" task :drop_sandboxes => :environment do Trade::AnnualReportUpload.where(:is_done => false).each do |aru| @@ -42,5 +50,4 @@ namespace :db do puts "Deleting annual report uploads & dropping sandboxes" Trade::AnnualReportUpload.all.each { |aru| aru.destroy } end - end