Merge branch 'development'

.travis.yml

@@ -47,7 +47,6 @@ jobs:
         - npm install
         - gem install bundler
         - bundle config --local build.sassc --disable-march-tune-native
-        - sudo bash -c 'echo -e "#define ACCEPT_USE_OF_DEPRECATED_PROJ_API_H\n$(cat /usr/include/proj_api.h)" > /usr/include/proj_api.h' # rgeo-proj4 incompatibility workaround
         - bundle install -j3 --without development production
       before_script:
         - echo ===[TEST_WORKER=$TEST_WORKER before_script $(date -u +%Y%m%d-%H%M%S)]===

.travis/docker-test.sh

@@ -24,5 +24,9 @@ for ver in `echo 10 12`; do
   # Test redis is running
   docker-compose exec taxonworks redis-cli ping
 
+  # Test deploy-time backup is restorable
+  docker-compose exec taxonworks find /backup | grep dump || (echo "BACKUP AT STARTUP WAS NOT MADE!" && exit 1) # Check backup was made at startup
+  docker-compose exec db psql -U travis -c "SELECT pg_terminate_backend(pg_stat_activity.pid) FROM pg_stat_activity WHERE pg_stat_activity.datname = 'travis' AND pid <> pg_backend_pid();"
+  docker-compose exec taxonworks bundle exec rake tw:db:restore_last DISABLE_DATABASE_ENVIRONMENT_CHECK=1
   docker-compose down --volumes
 done

CHANGELOG.md

@@ -9,9 +9,68 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
-## [0.13.0] - 2020-09-22
+## [0.14.0] - 2020-10-16
 
 ### Added
+- Collecting Event API endpoints
+- Collection Object API endpoints
+- Biological Assertion API endpoints
+- Asserted Distribution API endpoints
+- New Otu API params
+- People filter API endpoints [#1509]
+- Identifier filter API endpoints [#1510]
+- Source filter API endpoints [#1511]
+- New Interactive Key task [#1810] 
+- New model for matrix based interactive keys which produce JSON for the Interactive Key task [#1810]
+- `weight` field to descriptor
+- Ancestors facet on filter nomenclature [#1791]
+- TW_DISABLE_DB_BACKUP_AT_DEPLOY_TIME env var to disable built-in backup functionality at deploy/database-update time.
+- Display coordinate type specimens [#1811]
+- Changed background color header for invalid names on Browse OTU
+- Taxonworks version in header bar when not running in sandbox mode
+
+### Fixed
+- Fixed radial navigator broken for some data [#1824]
+- Fixed IsData position [#1805]
+- Collecting event object radial metadata settings
+- Webpack resolved_paths deprecation warning
+- Missing /otus/:otu_id/taxon_determinations route
+- tw:db:restore task not picking up database host settings
+- Create citation on new combination without pages
+- Param descriptor id on new descriptor task [#1798]
+- Filter by user on filter nomenclature [#1780]
+- Optimized selector queries for Loan model
+
+### Changed
+- Fix original author string for Plant names
+- Additional date format added for date recognition RegEx
+- Removed some attributes from api/v1 endpoints to simplify responses
+- type_materials/:id.json includes `original_combination` string
+- CoLDP references are full cached values, not partially passed
+- Combination nomenclatural code inference drawn from members, not parent
+- Some nomenclature rank related simbols moved to constants
+- Load Images for coordinate OTUs [#1787]
+- Extended New Image task upload timeout from 30 seconds to 10 minutes
+- Updated rgeo-proj4 gem
+
+
+[#1824]: https://github.com/SpeciesFileGroup/taxonworks/issues/1824
+[#1805]: https://github.com/SpeciesFileGroup/taxonworks/issues/1805
+[#1509]: https://github.com/SpeciesFileGroup/taxonworks/issues/1509
+[#1510]: https://github.com/SpeciesFileGroup/taxonworks/issues/1510
+[#1511]: https://github.com/SpeciesFileGroup/taxonworks/issues/1511
+[#1780]: https://github.com/SpeciesFileGroup/taxonworks/issues/1780
+[#1791]: https://github.com/SpeciesFileGroup/taxonworks/issues/1791 
+[#1787]: https://github.com/SpeciesFileGroup/taxonworks/issues/1787
+[#1798]: https://github.com/SpeciesFileGroup/taxonworks/issues/1798
+[#1810]: https://github.com/SpeciesFileGroup/taxonworks/pull/1810
+[#1811]: https://github.com/SpeciesFileGroup/taxonworks/issues/1811
+
+## [0.13.0] - 2020-09-22
+
+### Changed
+- Removed forced dependency on google-protobuf gem
+- Updated gems
 - Browse OTU page unifies coordinate OTUs for Asserted Distribution and Biological Associations [#1570]
 - Handling for new unicode minutes, seconds symbols [#1526]
 - Descriptor object radial paths
@@ -504,7 +563,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
 
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.13.0...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.14.0...development
+[0.14.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.13.0...v0.14.0
 [0.13.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.17...v0.13.0
 [0.12.17]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.16...v0.12.17
 [0.12.16]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.15...v0.12.16

Gemfile

@@ -6,9 +6,6 @@ ruby '2.7.1'
 
 gem 'bundler', '~> 2.0'
 
-# TODO: Remove when solved without forcing
-gem 'google-protobuf', '~> 3.12.0.rc.1'
-
 gem 'rake', '~> 13.0'
 gem 'rails', '~> 6.0'
 gem 'pg', '~> 1.1'

Gemfile.lock

@@ -9,7 +9,7 @@ GIT
 
 GIT
   remote: https://github.com/LocoDelAssembly/biodiversity.git
-  revision: 1c44d3d49c3a2cb4905f29c8dfac0beea6ff0a02
+  revision: 46d727e87610b9aad933250ecee002c83be8b2be
   branch: ipc-mode-rc1
   specs:
     biodiversity (4.1.0)
@@ -192,16 +192,16 @@ GEM
     gnfinder (0.11.0)
       grpc (~> 1.28)
       grpc-tools (~> 1.28)
-    google-protobuf (3.12.4)
+    google-protobuf (3.13.0)
     googleapis-common-protos-types (1.0.5)
       google-protobuf (~> 3.11)
     gpx (1.0.0)
       nokogiri (~> 1.7)
       rake
     groupdate (4.3.0)
       activesupport (>= 5)
-    grpc (1.31.1)
-      google-protobuf (~> 3.12)
+    grpc (1.32.0)
+      google-protobuf (~> 3.13)
       googleapis-common-protos-types (~> 1.0)
     grpc-tools (1.32.0)
     guard (2.16.2)
@@ -395,7 +395,7 @@ GEM
       rgeo (>= 1.0.0)
     rgeo-geojson (2.1.1)
       rgeo (>= 1.0.0)
-    rgeo-proj4 (2.0.0)
+    rgeo-proj4 (2.0.1)
       rgeo (~> 2.0)
     rmagick (4.1.2)
     rspec (3.9.0)
@@ -424,7 +424,7 @@ GEM
       rspec-support (~> 3.9)
     rspec-support (3.9.3)
     rtesseract (3.1.2)
-    rubocop (0.91.0)
+    rubocop (0.91.1)
       parallel (~> 1.10)
       parser (>= 2.7.1.1)
       rainbow (>= 2.2.2, < 4.0)
@@ -592,7 +592,6 @@ DEPENDENCIES
   ffi-geos (~> 2.1.0)
   geckodriver-helper!
   gnfinder (~> 0.11.0)
-  google-protobuf (~> 3.12.0.rc.1)
   gpx (~> 1.0.0)
   groupdate (~> 4.2)
   guard-rspec (~> 4.7.3)

README.md

@@ -24,7 +24,7 @@ TaxonWorks is open source and is presently available under the [University of Il
 
 ## Funding
 
-The foundation of TaxonWorks is funded by an endowment of the Species File Group. This project was funded in part by NSF-ABI-1356381.  Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. 
+The foundation of TaxonWorks is funded by an endowment of the [Species File Group](21). This project was funded in part by NSF-ABI-1356381.  Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. 
 
 [1]: https://travis-ci.org/SpeciesFileGroup/taxonworks.svg?branch=development
 [2]: https://travis-ci.org/SpeciesFileGroup/taxonworks
@@ -41,4 +41,5 @@ The foundation of TaxonWorks is funded by an endowment of the Species File Group
 [18]: https://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License
 [19]: https://gitter.im/SpeciesFileGroup/taxonworks?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge
 [20]: https://badges.gitter.im/SpeciesFileGroup/taxonworks.svg
+[21]: https://speciesfilegroup.org
 

app/assets/stylesheets/base/headers.scss

@@ -6,10 +6,6 @@
   background-color: $color-header;
   height: 50px;
 
-  a {
-    padding: $standard_padding;
-  }
-
   #taxonworks {
     .logo {
       width: 160px;
@@ -23,12 +19,19 @@
     }
   }
 
+  #taxonworks_version {
+    color: White;
+    font-size: $font_small;
+    line-height: $font_small;
+    text-decoration: none;
+    padding: 0;
+  }
+
   #session_nav {
     flex-grow: 0;
     a {
       padding: 0px;
       color: #FFF;
-
     }
     li {
       padding-left: $standard_padding;

app/assets/stylesheets/views/tasks/matrix/observation_matrices.scss

@@ -23,3 +23,73 @@
   position: relative;
   text-align: left;
 }
+
+#vue-interactive-keys {
+  height: calc(100vh - 220px);
+  max-height: calc(100vh - 220px);
+
+  .header-bar {
+    width: 100%;
+    height: 50px;
+    border-bottom: 1px solid #CCCCCC;
+    background-color: white;
+  }
+
+  .i3-grid {
+    display: grid;
+    grid-template-columns: repeat(2, 1fr);
+    grid-template-rows: repeat(2, 1fr);
+    grid-column-gap: 0px;
+    grid-row-gap: 0px;
+    background-color: #CCCCCC;
+    grid-gap: 1px;
+  }
+  .grid-icon {
+    width: 20px;
+    height: 12px;
+    border: 2px solid transparent;
+    background-color: transparent;
+    grid-gap: 2px;
+  }
+  .grid-item {
+    background-color: white;
+    overflow: scroll;
+  }
+
+  .layout-mode-1 {
+    .descriptors-view { 
+      grid-area: 1 / 1 / 2 / 3; 
+    }
+    .taxa-remaining { 
+      grid-area: 2 / 1 / 3 / 2; 
+    }
+    .taxa-eliminated { 
+      grid-area: 2 / 2 / 3 / 3;
+    }
+  }
+
+  .layout-mode-2 {
+    .descriptors-view  { 
+      grid-area: 1 / 1 / 3 / 2; 
+    }
+    .taxa-remaining { 
+      grid-area: 1 / 2 / 2 / 3; 
+    }
+    .taxa-eliminated { 
+      grid-area: 2 / 2 / 3 / 3; 
+    }
+  }
+
+  .full-height {
+    height: 100%;
+  }
+
+  .mainfont { color: #004050;}
+  .red { color: #C00000; }
+  .redbold { color: #C00000; font-weight: bold; }
+
+  .i3 {
+    box-shadow: 0px 2px 2px 0px rgba(0,0,0,0.2);
+  }
+
+}

app/controllers/api_controller.rb

@@ -12,7 +12,6 @@ class ApiController < ActionController::API
     include RequestType
     include PaginationHeaders
 
-
     # attr_accessor :permitted_projects
     # before_action :set_permitted_projects
 

app/controllers/asserted_distributions_controller.rb

@@ -1,7 +1,7 @@
 class AssertedDistributionsController < ApplicationController
   include DataControllerConfiguration::ProjectDataControllerConfiguration
 
-  before_action :set_asserted_distribution, only: [:show, :edit, :update, :destroy]
+  before_action :set_asserted_distribution, only: [:show, :edit, :update, :destroy, :api_show]
 
   # GET /asserted_distributions
   # GET /asserted_distributions.json
@@ -99,9 +99,10 @@ def search
 
   # GET /asserted_distributions/download
   def download
-    send_data(Export::Download.generate_csv(AssertedDistribution.where(project_id: sessions_current_project_id)),
-              type: 'text',
-              filename: "asserted_distributions_#{DateTime.now}.csv")
+    send_data(
+      Export::Download.generate_csv(AssertedDistribution.where(project_id: sessions_current_project_id)),
+      type: 'text',
+      filename: "asserted_distributions_#{DateTime.now}.csv")
   end
 
   # GET /asserted_distributions/batch_load
@@ -134,10 +135,24 @@ def create_simple_batch_load
     render :batch_load
   end
 
+  def api_index
+    @asserted_distributions = Queries::AssertedDistribution::Filter.new(api_params)
+      .all
+      .where(project_id: sessions_current_project_id)
+      .order('asserted_distributions.id')
+      .page(params[:page])
+      .per(params[:per] || 100)
+    render '/asserted_distributions/api/v1/index'
+  end
+
+  def api_show
+    render '/asserted_distributions/api/v1/show'
+  end
+
   private
 
   def set_asserted_distribution
-    @asserted_distribution = AssertedDistribution.with_project_id(sessions_current_project_id).find(params[:id])
+    @asserted_distribution = AssertedDistribution.where(project_id: sessions_current_project_id).find(params[:id])
     @recent_object = @asserted_distribution
   end
 
@@ -161,4 +176,9 @@ def filter_params
     params.permit(:otu_id, :geographic_area_id, :recent, otu_id: [], geographic_area_id: [])
   end
 
+  def api_params
+    params.permit(:otu_id, :geographic_area_id, :recent, :geo_json)
+  end
+
+
 end