Merge branch 'development'

.github/docker-tests/docker-image-test/Dockerfile

@@ -5,7 +5,7 @@ RUN apt-get install -y curl bzip2 unzip default-jre \
                        libgtk-3-0 libgtk-3-dev libdbus-glib-1-2 libxt6 # Firefox requirements
 
 RUN curl -sL 'https://download.mozilla.org/?product=firefox-latest-ssl&os=linux64&lang=en-US' | \
-    tar -xjf - -C /usr/bin
+    tar -xJf - -C /usr/bin
 
 RUN /usr/bin/firefox/firefox --version
 

.github/workflows/build.yml

@@ -66,18 +66,18 @@ jobs:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('.ruby-version', '**/Gemfile', '**/Gemfile.lock', 'exe/install-imagemagick7.sh') }}
 
-    - name: Set up Node 18 LTS
+    - name: Set up Node 22 LTS
       uses: actions/setup-node@v4
       with:
-        node-version: '18'
+        node-version: '22'
 
     - name: Set up Node packages cache
       uses: actions/cache@v4
       with:
         path: |
           ~/.npm
           **/node_modules
-        key: ${{ runner.os }}-node-18-${{ hashFiles('**/package-lock.json') }}
+        key: ${{ runner.os }}-node-22-${{ hashFiles('**/package-lock.json') }}
 
     - name: Set up assets cache
       uses: actions/cache@v4

.ruby-version

@@ -1 +1 @@
-3.3.4
+3.3.6

CHANGELOG.md

@@ -9,6 +9,74 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.47.0] - 2025-02-06
+
+### Added
+
+- Use Rails 7.2 and Ruby 3.3.6
+- New image task: Add field occurrence to depict some list [#4135]
+- Grab cursor to make sorting feature visible [#4153]
+- API endpoint for image matrix
+- Order of depictions coming from the image matrix
+- Hub tasks: Add visual effect for fav icons and tooltip for categories [#4177]
+- Distribution to COLDP exports [#3148]
+- Taxon links to COLDP exports
+- SpeciesInteraction to COLDP exports [#3158]
+- Specs and optimizations to COLDP
+- Pull metadata from ChecklistBank in order to merge updated metadata into COLDP exports
+- Filter's match identifiers facet can now be quickly accessed with `shift-ctrl-m` in a modal form
+- `gift` facet to Filter loans.
+- Multi data attribute update task [#4142]
+- Keys are now multifurcatable [#4148]
+- Identical Document validation
+- Some inline help and visual improvements [#4177]
+- Keys can be cloned, merged, and inserted to [#4056]
+- API endpoint for serving Image matrices
+
+### Changed
+
+- Match identifiers defaults to match Identifier, not internal, `\n`, and caseless match [#4176]
+- Added Gift status notices to loans form [#4174]
+- Improved and clarified DwcOccurrence indexing concepts and application
+- Improved writing to cached* fields for TaxonName 
+
+### Fixed
+
+- Fixes to TaxonWorks CSL style 
+- Bug in Image autocomplete
+- CatalogNumbers attached to Containers not appearing in CollectionObject tag [#4163]
+- OriginRelationship creation for Sequences [#4180]
+- CSD: change of namespace not updating [#4147]
+- TaxonWorks bibliography style for book chapter.
+- Removed obsolete Description table from COLDP exports
+- Remove [sic] from COLDP name fields [#3833]
+- Autonym synonyms bug in COLDP exporter [#4175]
+- New taxon name: Show only subject relationships on Relationships section
+- Images added before saving field occurrence are not saved [#4134]
+- Rendering Family group names from invalid names [#4187]
+- Verbatim latitude not displaying [#4178]
+
+
+[#4056]: https://github.com/SpeciesFileGroup/taxonworks/issues/4056
+[#4177]: https://github.com/SpeciesFileGroup/taxonworks/issues/4177
+[#4178]: https://github.com/SpeciesFileGroup/taxonworks/issues/4178
+[#4148]: https://github.com/SpeciesFileGroup/taxonworks/issues/4148
+[#4163]: https://github.com/SpeciesFileGroup/taxonworks/issues/4163
+[#4174]: https://github.com/SpeciesFileGroup/taxonworks/issues/4174
+[#4176]: https://github.com/SpeciesFileGroup/taxonworks/issues/4176
+[#4180]: https://github.com/SpeciesFileGroup/taxonworks/issues/4180
+[#3148]: https://github.com/SpeciesFileGroup/taxonworks/issues/3148
+[#3158]: https://github.com/SpeciesFileGroup/taxonworks/issues/3158
+[#3833]: https://github.com/SpeciesFileGroup/taxonworks/issues/3833
+[#4134]: https://github.com/SpeciesFileGroup/taxonworks/issues/4134
+[#4135]: https://github.com/SpeciesFileGroup/taxonworks/issues/4135
+[#4142]: https://github.com/SpeciesFileGroup/taxonworks/issues/4142
+[#4147]: https://github.com/SpeciesFileGroup/taxonworks/issues/4147
+[#4153]: https://github.com/SpeciesFileGroup/taxonworks/issues/4153
+[#4175]: https://github.com/SpeciesFileGroup/taxonworks/issues/4175
+[#4177]: https://github.com/SpeciesFileGroup/taxonworks/issues/4177
+[#4187]: https://github.com/SpeciesFileGroup/taxonworks/issues/4187
+
 ## [0.46.1] - 2024-12-04
 
 ### Fixed
@@ -339,6 +407,10 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3996]: https://github.com/SpeciesFileGroup/taxonworks/issues/3996
 [#3997]: https://github.com/SpeciesFileGroup/taxonworks/issues/3997
 
+### Fixed
+
+- Handling of [sic] in Protonym#original_combination_infraspecific_element [#3867]
+
 ## [0.42.0] - 2024-06-28
 
 ### Added
@@ -701,6 +773,7 @@ _Special thanks to Tom Klein for his amazing open-source contributions on this r
 [#3774]: https://github.com/SpeciesFileGroup/taxonworks/issues/3774
 [#3794]: https://github.com/SpeciesFileGroup/taxonworks/issues/3794
 [#3824]: https://github.com/SpeciesFileGroup/taxonworks/issues/3824
+[#3833]: https://github.com/SpeciesFileGroup/taxonworks/issues/3833
 
 ## [0.38.2] - 2024-02-09
 
@@ -5003,7 +5076,8 @@ _Special thanks to Tom Klein for his amazing open-source contributions on this r
 - Loosing input page numbers when switching tabs on New Taxon Name task
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.46.1..development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.47.0..development
+[0.47.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.46.1...v0.47.0
 [0.46.1]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.46.0...v0.46.1
 [0.46.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.45.0...v0.46.0
 [0.45.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.44.3...v0.45.0

Dockerfile

@@ -58,13 +58,11 @@ FROM base AS assets-precompiler
 
 # http://blog.zeit.io/use-a-fake-db-adapter-to-play-nice-with-rails-assets-precompilation/
 RUN bundle add activerecord-nulldb-adapter
-RUN printf "production:\n  adapter: nulldb" > config/database.yml \
-&&  printf "production:\n  secret_key_base: $(bundle exec rails secret)" > config/secrets.yml
+RUN printf "production:\n  adapter: nulldb" > config/database.yml
 
 # Precompiling and also removing config files just in case someone uses `docker build --target=assets-precompiler`
-
-RUN NODE_OPTIONS="--max-old-space-size=4096" bundle exec rake assets:precompile \
-&& rm config/database.yml config/secrets.yml
+RUN NODE_OPTIONS="--max-old-space-size=4096" SECRET_KEY_BASE="$(bundle exec rails secret)" bundle exec rake assets:precompile \
+&& rm config/database.yml
 
 FROM base
 COPY --from=assets-precompiler --chown=9999:9999 /app/public /app/public

Dockerfile.base

@@ -2,15 +2,16 @@ FROM phusion/passenger-ruby33:latest AS base
 ARG MAKE_JOBS=3
 
 # From Phusion
-ENV HOME /root
+ENV HOME=/root
 RUN rm /etc/nginx/sites-enabled/default
 ADD config/docker/nginx/gzip_max.conf /etc/nginx/conf.d/gzip_max.conf
 
 # TaxonWorks dependencies
 COPY exe/install-imagemagick7.sh /usr/local/bin
 RUN echo "deb https://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list && \
       curl -sL https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add - && \
-      echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_18.x nodistro main" > /etc/apt/sources.list.d/nodesource.list && \
+      echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_22.x nodistro main" > /etc/apt/sources.list.d/nodesource.list && \
+      sed -i 's/^Types: deb$/Types: deb deb-src/' /etc/apt/sources.list.d/ubuntu.sources && \
       apt update && apt-get install -y locales software-properties-common \
                          postgresql-client-16 \
                          build-essential autoconf libtool git-core jq \
@@ -28,21 +29,22 @@ RUN echo "deb https://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg m
 
 RUN locale-gen en_US.UTF-8
 
-ENV LANG en_US.UTF-8
-ENV LANGUAGE en_US:en
-ENV LC_ALL en_US.UTF-8
+ENV LANG=en_US.UTF-8
+ENV LANGUAGE=en_US:en
+ENV LC_ALL=en_US.UTF-8
 
 RUN echo 'gem: --no-rdoc --no-ri >> "$HOME/.gemrc"'
 RUN gem update --system
 RUN gem install bundler
 
-FROM ubuntu:22.04 AS imagemagick
+FROM ubuntu:24.04 AS imagemagick
 RUN apt-get update && apt-get install -y imagemagick
 
 FROM base
 COPY --from=imagemagick /etc/ImageMagick-6 /usr/local/etc/ImageMagick-7
 
 # Set up ImageMagick
-RUN sed -i 's/name="disk" value="1GiB"/name="disk" value="8GiB"/' /usr/local/etc/ImageMagick-7/policy.xml && \
+RUN sed -i 's/name="disk" value="2GiB"/name="disk" value="8GiB"/' /usr/local/etc/ImageMagick-7/policy.xml && \
+identify -list resource && \
       identify -list resource | grep Disk | grep 8GiB && magick -list format | grep "HEIC      rw+" # Confirm HEIC support and that 8GB disk setting is active
 

Dockerfile.development

@@ -4,9 +4,9 @@ ARG BUNDLER_WORKERS=1
 # Install Firefox (for headless feature tests)
 RUN apt-get update && \
     apt-get install -y locales \
-                       libgtk-3-0 libgtk-3-dev libdbus-glib-1-2 libxt6 libasound2 && \
+                       libgtk-3-0 libgtk-3-dev libdbus-glib-1-2 libxt6 libasound2t64 && \
     curl -sL 'https://download.mozilla.org/?product=firefox-latest&lang=en-US&os=linux64' | \
-    tar -xjf - -C /usr/bin && \
+    tar -xJf - -C /usr/bin && \
     /usr/bin/firefox/firefox --version && \
     apt clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

Gemfile

@@ -7,9 +7,9 @@ ruby '>= 3.2', '< 3.4.0'
 gem 'bundler', '~> 2.5'
 
 gem 'rake', '~> 13.0'
-gem 'rails', '~> 7.1'
+gem 'rails', '~> 7.2'
 gem 'pg', '~> 1.1'
-gem 'activerecord-postgis-adapter', '~> 9.0'
+gem 'activerecord-postgis-adapter', '~> 10.0'
 gem 'hiredis', '~> 0.6.1'
 gem 'redis', '~> 4.5'
 gem 'bootsnap', require: false
@@ -101,7 +101,7 @@ gem 'rails-jquery-autocomplete', '~> 1.0.3'
 
 gem 'turbolinks', '~> 5.2.0'
 gem 'jquery-turbolinks', '~> 2.1'
-gem 'shakapacker', '8.0.2'
+gem 'shakapacker', '8.1.0'
 
 # BibTeX handling
 gem 'csl', '~> 2.0'