From b99a7dbfa71c53baf5ed0253234335aa07024442 Mon Sep 17 00:00:00 2001 From: mjy Date: Fri, 26 Apr 2024 08:51:19 -0500 Subject: [PATCH 01/10] Fix OTU autocomplete raise --- CHANGELOG.md | 4 ++++ lib/queries/otu/autocomplete.rb | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5dc03b4ec2..ae1dc16c5a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,10 @@ This project does not yet adheres to [Semantic Versioning](https://semv ## [unreleased] +### Fixed + +- OTU autocomplete raises when no taxon names match + \- ## [0.40.5] - 2024-04-25 diff --git a/lib/queries/otu/autocomplete.rb b/lib/queries/otu/autocomplete.rb index dd434ddc88..0523faa584 100644 --- a/lib/queries/otu/autocomplete.rb +++ b/lib/queries/otu/autocomplete.rb @@ -145,7 +145,7 @@ def autocomplete_taxon_name_extended ] } - return nil if ids.empty? + return ::Otu.none if ids.empty? ids.uniq! From e29c199409f5d33c855231c4c7773408238b4e47 Mon Sep 17 00:00:00 2001 From: mjy Date: Fri, 26 Apr 2024 12:34:29 -0500 Subject: [PATCH 02/10] Notes params on Source filtering. Fix #3927 --- CHANGELOG.md | 3 ++- lib/queries/source/filter.rb | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ae1dc16c5a..bf709e4eaa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,9 +9,10 @@ This project does not yet adheres to [Semantic Versioning](https://semv ### Fixed +- Notes params not applied in Source filters (anywhere) [#3927] - OTU autocomplete raises when no taxon names match -\- +[#3927]: https://github.com/SpeciesFileGroup/taxonworks/issues/3927 ## [0.40.5] - 2024-04-25 diff --git a/lib/queries/source/filter.rb b/lib/queries/source/filter.rb index f6cacd1c8a..8b08944c9f 100644 --- a/lib/queries/source/filter.rb +++ b/lib/queries/source/filter.rb @@ -189,6 +189,7 @@ def initialize(query_params) set_attributes_params(params) set_empty_params(params) set_tags_params(params) + set_notes_params(params) set_user_dates(params) end From 4c67014e77abc88489d104cfebb7c4bb3ec419eb Mon Sep 17 00:00:00 2001 From: jlpereira Date: Fri, 26 Apr 2024 17:36:47 -0300 Subject: [PATCH 03/10] Fix catalog number panel --- CHANGELOG.md | 4 +- .../catalogueNumber/catalogNumber.vue | 214 ++++++++---------- 2 files changed, 98 insertions(+), 120 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bf709e4eaa..62b6299501 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ This project does not yet adheres to [Semantic Versioning](https://semv - Notes params not applied in Source filters (anywhere) [#3927] - OTU autocomplete raises when no taxon names match +- CSD: Catalog number panel displays warning messages when the namespace is set [#3927]: https://github.com/SpeciesFileGroup/taxonworks/issues/3927 @@ -20,7 +21,7 @@ This project does not yet adheres to [Semantic Versioning](https://semv - `/api/v1/taxon_name_relationships.csv` endpoint -### Changed +### Changed - Dwca `otu_name` only includes Otu#name, never anything else. - `api/v1/otus/autocomplete` now more acurately returns the label of the matching term, i.e. Combinations are supported in rendering [https://github.com/SpeciesFileGroup/taxonpages/issues/193] @@ -34,7 +35,6 @@ This project does not yet adheres to [Semantic Versioning](https://semv - Basic endemism task had a broken link out - Prevent raise on bad polygon (LinearRing) Georeferences - [#3926]: https://github.com/SpeciesFileGroup/taxonworks/issues/3926 ## [0.40.4] - 2024-04-21 diff --git a/app/javascript/vue/tasks/digitize/components/catalogueNumber/catalogNumber.vue b/app/javascript/vue/tasks/digitize/components/catalogueNumber/catalogNumber.vue index b9f5470049..1570e03f45 100644 --- a/app/javascript/vue/tasks/digitize/components/catalogueNumber/catalogNumber.vue +++ b/app/javascript/vue/tasks/digitize/components/catalogueNumber/catalogNumber.vue @@ -102,7 +102,7 @@ - From 64dd712c8693dc3107e84dbb616c3b0d8b61c227 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?= Date: Sat, 27 Apr 2024 20:20:50 -0300 Subject: [PATCH 04/10] Revert "Temporary fix for IRB warning in container images" This reverts commit 88f65091852cd0ebc95306af007a43fc782335b4. --- Dockerfile.base | 5 ----- 1 file changed, 5 deletions(-) diff --git a/Dockerfile.base b/Dockerfile.base index b82d808bd6..29648ee2ad 100644 --- a/Dockerfile.base +++ b/Dockerfile.base @@ -45,8 +45,3 @@ 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 && \ identify -list resource | grep Disk | grep 8GiB && magick -list format | grep "HEIC rw+" # Confirm HEIC support and that 8GB disk setting is active - -# Workaround for https://github.com/phusion/passenger-docker/issues/393 / https://github.com/rvm/rvm/issues/5449 -RUN sed -i 's/require/load/g' /usr/local/rvm/rubies/ruby-3.3.0/.irbrc -# Yes, no dot -RUN touch /root/irbrc && touch /home/app/irbrc \ No newline at end of file From b0a2f7d00a391e238ce5778f5dd2e0943bd74473 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?= Date: Sat, 27 Apr 2024 20:39:48 -0300 Subject: [PATCH 05/10] Updated actions version in base image workflow [skip ci] --- .github/workflows/base-image.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/base-image.yml b/.github/workflows/base-image.yml index 06077e239f..b12e1d8f3b 100644 --- a/.github/workflows/base-image.yml +++ b/.github/workflows/base-image.yml @@ -12,14 +12,14 @@ jobs: steps: - name: Git checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Build the Docker image run: docker build -f Dockerfile.base . -t sfgrp/taxonworks-base - name: Login to DockerHub if: ${{ github.event_name != 'pull_request' }} - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: username: ${{ secrets.DOCKERHUB_USERNAME }} password: ${{ secrets.DOCKERHUB_TOKEN }} From 80713463321eb456e0126ff81864bcd170f25912 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?= Date: Mon, 29 Apr 2024 09:35:18 -0300 Subject: [PATCH 06/10] Revert "Revert "Temporary fix for IRB warning in container images"" This reverts commit 64dd712c8693dc3107e84dbb616c3b0d8b61c227. --- Dockerfile.base | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/Dockerfile.base b/Dockerfile.base index 29648ee2ad..b82d808bd6 100644 --- a/Dockerfile.base +++ b/Dockerfile.base @@ -45,3 +45,8 @@ 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 && \ identify -list resource | grep Disk | grep 8GiB && magick -list format | grep "HEIC rw+" # Confirm HEIC support and that 8GB disk setting is active + +# Workaround for https://github.com/phusion/passenger-docker/issues/393 / https://github.com/rvm/rvm/issues/5449 +RUN sed -i 's/require/load/g' /usr/local/rvm/rubies/ruby-3.3.0/.irbrc +# Yes, no dot +RUN touch /root/irbrc && touch /home/app/irbrc \ No newline at end of file From df8d65f3ec29bcd72bc9e53ad520eed0b8bedab7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?= Date: Mon, 29 Apr 2024 09:50:06 -0300 Subject: [PATCH 07/10] Updated temporary fix for IRB warning in container images to Ruby 3.3.1 [skip ci] --- Dockerfile.base | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile.base b/Dockerfile.base index b82d808bd6..adc0bec838 100644 --- a/Dockerfile.base +++ b/Dockerfile.base @@ -47,6 +47,6 @@ RUN sed -i 's/name="disk" value="1GiB"/name="disk" value="8GiB"/' /usr/local/etc identify -list resource | grep Disk | grep 8GiB && magick -list format | grep "HEIC rw+" # Confirm HEIC support and that 8GB disk setting is active # Workaround for https://github.com/phusion/passenger-docker/issues/393 / https://github.com/rvm/rvm/issues/5449 -RUN sed -i 's/require/load/g' /usr/local/rvm/rubies/ruby-3.3.0/.irbrc +RUN sed -i 's/require/load/g' /usr/local/rvm/rubies/ruby-3.3.1/.irbrc # Yes, no dot -RUN touch /root/irbrc && touch /home/app/irbrc \ No newline at end of file +RUN touch /root/irbrc && touch /home/app/irbrc From 72e118b618b91d8235dff5fa7015cb259ddeee06 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?= Date: Mon, 29 Apr 2024 10:04:30 -0300 Subject: [PATCH 08/10] bundle update --- CHANGELOG.md | 4 ++++ Gemfile.lock | 10 +++++----- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bf709e4eaa..3bdbce33cc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,10 @@ This project does not yet adheres to [Semantic Versioning](https://semv ## [unreleased] +### Changed + +- Updated Ruby gems + ### Fixed - Notes params not applied in Source filters (anywhere) [#3927] diff --git a/Gemfile.lock b/Gemfile.lock index 77c5d5536d..40a874863e 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -292,7 +292,7 @@ GEM concurrent-ruby (~> 1.0) indefinite_article (0.2.5) activesupport - jbuilder (2.11.5) + jbuilder (2.12.0) actionview (>= 5.0.0) activesupport (>= 5.0.0) jquery-rails (4.6.0) @@ -380,9 +380,9 @@ GEM paperclip-meta (3.1.0) paperclip (>= 5.0) parallel (1.24.0) - parallel_tests (4.7.0) + parallel_tests (4.7.1) parallel - parser (3.3.0.5) + parser (3.3.1.0) ast (~> 2.4.1) racc parslet (2.0.0) @@ -526,7 +526,7 @@ GEM rspec-support (~> 3.10) rspec-support (3.13.1) rtesseract (3.1.3) - rubocop (1.63.3) + rubocop (1.63.4) json (~> 2.3) language_server-protocol (>= 3.17.0) parallel (~> 1.10) @@ -581,7 +581,7 @@ GEM rdoc (>= 5.0) seedbank (0.5.0) rake (>= 10.0) - selenium-webdriver (4.19.0) + selenium-webdriver (4.20.1) base64 (~> 0.2) rexml (~> 3.2, >= 3.2.5) rubyzip (>= 1.2.2, < 3.0) From 947968e14b2a8f88c632203ee7f0eeb8da18e137 Mon Sep 17 00:00:00 2001 From: jlpereira Date: Mon, 29 Apr 2024 11:11:58 -0300 Subject: [PATCH 09/10] Update packages --- package-lock.json | 226 +++++++++++++++++++++++----------------------- package.json | 6 +- 2 files changed, 116 insertions(+), 116 deletions(-) diff --git a/package-lock.json b/package-lock.json index c2a04c3d1e..b7a41bbc3f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -20,7 +20,7 @@ "axios": "^1.6.8", "chart.js": "^4.4.2", "d3": "^7.9.0", - "dompurify": "^3.1.0", + "dompurify": "^3.1.1", "easymde": "^2.18.0", "exif-js": "^2.3.0", "leaflet": "^1.9.4", @@ -33,7 +33,7 @@ "shakapacker": "7.2.3", "v-hotkey": "^0.9.0", "v-network-graph": "^0.9.15", - "vue": "^3.4.25", + "vue": "^3.4.26", "vue-handy-scroll": "^3.0.2", "vue-tippy": "^6.4.1", "vue-turbolinks": "^2.2.2", @@ -47,7 +47,7 @@ "@babel/plugin-transform-runtime": "^7.24.3", "@babel/preset-env": "^7.24.4", "@babel/runtime": "^7.24.4", - "@vue/compiler-sfc": "^3.4.25", + "@vue/compiler-sfc": "^3.4.26", "babel-loader": "^9.1.3", "compression-webpack-plugin": "^11.1.0", "css-loader": "^7.1.1", @@ -3728,36 +3728,36 @@ "integrity": "sha512-9iXjMH9da+sfU3LhJ11X7n+HdhfwVa4R/AvhtSr6w9W1IGPDkeH+L+YHt5PLFRYcbWCviAg23Kicidc/qTdahw==" }, "node_modules/@vue/compiler-core": { - "version": "3.4.25", - "resolved": "https://registry.npmjs.org/@vue/compiler-core/-/compiler-core-3.4.25.tgz", - "integrity": "sha512-Y2pLLopaElgWnMNolgG8w3C5nNUVev80L7hdQ5iIKPtMJvhVpG0zhnBG/g3UajJmZdvW0fktyZTotEHD1Srhbg==", + "version": "3.4.26", + "resolved": "https://registry.npmjs.org/@vue/compiler-core/-/compiler-core-3.4.26.tgz", + "integrity": "sha512-N9Vil6Hvw7NaiyFUFBPXrAyETIGlQ8KcFMkyk6hW1Cl6NvoqvP+Y8p1Eqvx+UdqsnrnI9+HMUEJegzia3mhXmQ==", "dependencies": { "@babel/parser": "^7.24.4", - 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"dompurify": "^3.1.0", + "dompurify": "^3.1.1", "easymde": "^2.18.0", "exif-js": "^2.3.0", "leaflet": "^1.9.4", @@ -27,7 +27,7 @@ "shakapacker": "7.2.3", "v-hotkey": "^0.9.0", "v-network-graph": "^0.9.15", - "vue": "^3.4.25", + "vue": "^3.4.26", "vue-handy-scroll": "^3.0.2", "vue-tippy": "^6.4.1", "vue-turbolinks": "^2.2.2", @@ -50,7 +50,7 @@ "@babel/plugin-transform-runtime": "^7.24.3", "@babel/preset-env": "^7.24.4", "@babel/runtime": "^7.24.4", - "@vue/compiler-sfc": "^3.4.25", + "@vue/compiler-sfc": "^3.4.26", "babel-loader": "^9.1.3", "compression-webpack-plugin": "^11.1.0", "css-loader": "^7.1.1", From 7d26300cc55c01f16f393349964e510ed5f695ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?= Date: Tue, 30 Apr 2024 09:18:36 -0300 Subject: [PATCH 10/10] Preparing for version 0.40.6 release [skip ci] --- CHANGELOG.md | 5 ++++- lib/taxonworks/version.rb | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 258d0b8b8a..0b3e8bca7a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ This project does not yet adheres to [Semantic Versioning](https://semv ## [unreleased] +## [0.40.6] - 2024-04-30 + ### Changed - Updated Ruby gems @@ -4559,7 +4561,8 @@ _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/v0.40.5...development +[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.6...development +[0.40.6]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.5...v0.40.6 [0.40.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.4...v0.40.5 [0.40.4]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.3...v0.40.4 [0.40.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.2...v0.40.3 diff --git a/lib/taxonworks/version.rb b/lib/taxonworks/version.rb index c55997753c..b849112ad5 100644 --- a/lib/taxonworks/version.rb +++ b/lib/taxonworks/version.rb @@ -1,3 +1,3 @@ module TaxonWorks - VERSION = "0.40.5" + VERSION = "0.40.6" end