Release 1.103 #2309

eweitz · 2025-10-07T19:19:33Z

No description provided.

Updating to production NeMO API (SCP-6047)

Bumps [rack](https://github.com/rack/rack) from 2.2.14 to 2.2.18. - [Release notes](https://github.com/rack/rack/releases) - [Changelog](https://github.com/rack/rack/blob/main/CHANGELOG.md) - [Commits](rack/rack@v2.2.14...v2.2.18) --- updated-dependencies: - dependency-name: rack dependency-version: 2.2.18 dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]>

…2.2.18 Bump rack from 2.2.14 to 2.2.18

Properly scope existing results query to given cluster (SCP-6053)

…gend.jsx Co-authored-by: Eric Weitz <[email protected]>

Global mass-assignment of scatter plot custom colors (SCP-6052)

Adding search options for data types (SCP-6051)

…kbox Fix default state for options checkbox, text select behavior (SCP-6051)

Bumps [rack](https://github.com/rack/rack) from 2.2.18 to 2.2.19. - [Release notes](https://github.com/rack/rack/releases) - [Changelog](https://github.com/rack/rack/blob/main/CHANGELOG.md) - [Commits](rack/rack@v2.2.18...v2.2.19) --- updated-dependencies: - dependency-name: rack dependency-version: 2.2.19 dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]>

…2.2.19 Bump rack from 2.2.18 to 2.2.19

eweitz · 2025-10-08T17:42:22Z

The build failure is a false positive:

bundler: failed to load command: bin/rails (bin/rails)
/usr/local/rvm/gems/ruby-3.4.2/gems/mongo-2.18.1/lib/mongo/server_selector/base.rb:285:in 'Mongo::ServerSelector::Base#select_server': No primary_preferred server is available in cluster: #<Cluster topology=Unknown[34.69.44.144:27017] servers=[#<Server address=34.69.44.144:27017 UNKNOWN>]> with timeout=30, LT=0.015 (Mongo::Error::NoServerAvailable)
	from /usr/local/rvm/gems/ruby-3.4.2/gems/mongo-2.18.1/lib/mongo/cluster.rb:977:in 'Mongo::Cluster#validate_session_support!'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/mongo-2.18.1/lib/mongo/client.rb:1221:in 'Mongo::Client#get_session!'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/mongo-2.18.1/lib/mongo/client.rb:1104:in 'Mongo::Client#get_session'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/mongo-2.18.1/lib/mongo/collection/view/iterable.rb:59:in 'Mongo::Collection::View::Iterable#each'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/mongoid-7.5.1/lib/mongoid/contextual/mongo.rb:152:in 'Mongoid::Contextual::Mongo#each'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/mongoid-7.5.1/lib/mongoid/contextual/mongo.rb:337:in 'Enumerable#map'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/mongoid-7.5.1/lib/mongoid/contextual/mongo.rb:337:in 'Mongoid::Contextual::Mongo#map'
	from /usr/local/rvm/rubies/ruby-3.4.2/lib/ruby/3.4.0/forwardable.rb:240:in 'Mongoid::Contextual#map'
	from /home/app/webapp/app/models/study_file.rb:65:in '<class:StudyFile>'
	from /home/app/webapp/app/models/study_file.rb:1:in '<main>'
	from /usr/local/rvm/rubies/ruby-3.4.2/lib/ruby/3.4.0/bundled_gems.rb:82:in 'Kernel.require'
	from /usr/local/rvm/rubies/ruby-3.4.2/lib/ruby/3.4.0/bundled_gems.rb:82:in 'block (2 levels) in Kernel#replace_require'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bootsnap-1.13.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:32:in 'Kernel#require'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/zeitwerk-2.7.1/lib/zeitwerk/core_ext/kernel.rb:26:in 'Object#require'
	from /home/app/webapp/app/models/study.rb:686:in 'block (2 levels) in <class:Study>'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/swagger-blocks-3.0.0/lib/swagger/blocks/node.rb:16:in 'BasicObject#instance_eval'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/swagger-blocks-3.0.0/lib/swagger/blocks/node.rb:16:in 'Swagger::Blocks::Node.call'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/swagger-blocks-3.0.0/lib/swagger/blocks/nodes/properties_node.rb:6:in 'Swagger::Blocks::Nodes::PropertiesNode#property'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/swagger-blocks-3.0.0/lib/swagger/blocks/nodes/schema_node.rb:17:in 'Swagger::Blocks::Nodes::SchemaNode#property'
	from /home/app/webapp/app/models/study.rb:682:in 'block in <class:Study>'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/swagger-blocks-3.0.0/lib/swagger/blocks/node.rb:16:in 'BasicObject#instance_eval'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/swagger-blocks-3.0.0/lib/swagger/blocks/node.rb:16:in 'Swagger::Blocks::Node.call'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/swagger-blocks-3.0.0/lib/swagger/blocks/class_methods.rb:52:in 'Swagger::Blocks::ClassMethods#swagger_schema'
	from /home/app/webapp/app/models/study.rb:613:in '<class:Study>'
	from /home/app/webapp/app/models/study.rb:1:in '<main>'
	from /usr/local/rvm/rubies/ruby-3.4.2/lib/ruby/3.4.0/bundled_gems.rb:82:in 'Kernel.require'
	from /usr/local/rvm/rubies/ruby-3.4.2/lib/ruby/3.4.0/bundled_gems.rb:82:in 'block (2 levels) in Kernel#replace_require'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bootsnap-1.13.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:32:in 'Kernel#require'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/zeitwerk-2.7.1/lib/zeitwerk/core_ext/kernel.rb:26:in 'Object#require'
	from /home/app/webapp/lib/study_cleanup_tools.rb:31:in 'StudyCleanupTools.destroy_all_studies_and_workspaces'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/railties-6.1.7.9/lib/rails/commands/runner/runner_command.rb:45:in '<main>'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/railties-6.1.7.9/lib/rails/commands/runner/runner_command.rb:45:in 'Kernel#eval'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/railties-6.1.7.9/lib/rails/commands/runner/runner_command.rb:45:in 'Rails::Command::RunnerCommand#perform'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/thor-1.4.0/lib/thor/command.rb:28:in 'Thor::Command#run'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/thor-1.4.0/lib/thor/invocation.rb:127:in 'Thor::Invocation#invoke_command'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/thor-1.4.0/lib/thor.rb:538:in 'Thor.dispatch'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/railties-6.1.7.9/lib/rails/command/base.rb:69:in 'Rails::Command::Base.perform'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/railties-6.1.7.9/lib/rails/command.rb:48:in 'Rails::Command.invoke'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/railties-6.1.7.9/lib/rails/commands.rb:18:in '<main>'
	from /usr/local/rvm/rubies/ruby-3.4.2/lib/ruby/3.4.0/bundled_gems.rb:82:in 'Kernel.require'
	from /usr/local/rvm/rubies/ruby-3.4.2/lib/ruby/3.4.0/bundled_gems.rb:82:in 'block (2 levels) in Kernel#replace_require'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bootsnap-1.13.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:32:in 'Kernel#require'
	from bin/rails:4:in '<top (required)>'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/cli/exec.rb:59:in 'Kernel.load'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/cli/exec.rb:59:in 'Bundler::CLI::Exec#kernel_load'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/cli/exec.rb:23:in 'Bundler::CLI::Exec#run'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/cli.rb:451:in 'Bundler::CLI#exec'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/vendor/thor/lib/thor/command.rb:28:in 'Bundler::Thor::Command#run'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in 'Bundler::Thor::Invocation#invoke_command'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/vendor/thor/lib/thor.rb:538:in 'Bundler::Thor.dispatch'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/cli.rb:35:in 'Bundler::CLI.dispatch'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/vendor/thor/lib/thor/base.rb:584:in 'Bundler::Thor::Base::ClassMethods#start'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/cli.rb:29:in 'Bundler::CLI.start'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/exe/bundle:28:in 'block in <top (required)>'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/lib/bundler/friendly_errors.rb:118:in 'Bundler.with_friendly_errors'
	from /usr/local/rvm/gems/ruby-3.4.2/gems/bundler-2.7.1/exe/bundle:20:in '<top (required)>'
	from /usr/local/rvm/rubies/ruby-3.4.2/lib/ruby/site_ruby/3.4.0/rubygems.rb:319:in 'Kernel#load'
	from /usr/local/rvm/rubies/ruby-3.4.2/lib/ruby/site_ruby/3.4.0/rubygems.rb:319:in 'Gem.activate_and_load_bin_path'
	from /usr/local/rvm/gems/ruby-3.4.2/bin/bundle:25:in '<main>'
	from /usr/local/rvm/gems/ruby-3.4.2/bin/ruby_executable_hooks:22:in 'Kernel#eval'
	from /usr/local/rvm/gems/ruby-3.4.2/bin/ruby_executable_hooks:22:in '<main>'
FAILED to delete studies and workspaces
Error: Process completed with exit code 1.

bistline and others added 25 commits September 23, 2025 15:11

Changing to production NeMO API, re-enabling tests

e4c42f0

removing TODO comments

68d054b

Merge pull request #2303 from broadinstitute/jb-prod-nemo-api

2f72dbb

Updating to production NeMO API (SCP-6047)

Allow upload of custom color manifest w/ global apply

a29ad7b

still working on tests

8c08388

properly scope existing results query to given cluster

2ade1ac

Merge pull request #2304 from broadinstitute/dependabot/bundler/rack-…

ff24b04

…2.2.18 Bump rack from 2.2.14 to 2.2.18

Running .delay calls in foreground

67c9191

Adding export button, global button in palette picker

139355c

Merge pull request #2305 from broadinstitute/jb-de-eligible-annot-bugfix

59ad462

Properly scope existing results query to given cluster (SCP-6053)

linting

d89bfdb

Adding data type search filter for raw counts, DE, spatial

852b709

Update app/javascript/components/visualization/controls/ScatterPlotLe…

2c3d8ec

…gend.jsx Co-authored-by: Eric Weitz <[email protected]>

Fixing Azul regression re: content-type header

c85bd40

performance tweaks, test updates

3ec1c1f

removing unused require

3173914

fixing search test regressions re: query counts

3b206a1

Merge pull request #2306 from broadinstitute/jb-custom-color-manifest

1301918

Global mass-assignment of scatter plot custom colors (SCP-6052)

Merge pull request #2307 from broadinstitute/jb-data-types-search

061829d

Adding search options for data types (SCP-6051)

Fix default state for options checkbox, text select behavior

f0cf1d9

simplifying isDefaultChecked

f7705ab

have clear search remove options

69ced8f

lowering HcaAzulClient::MAX_RESILTS re: 502 errors

70c95c3

Merge pull request #2308 from broadinstitute/jb-data-type-search-chec…

1ea0d6b

…kbox Fix default state for options checkbox, text select behavior (SCP-6051)

eweitz requested a review from bistline October 7, 2025 19:19

bistline approved these changes Oct 8, 2025

View reviewed changes

Merge pull request #2310 from broadinstitute/dependabot/bundler/rack-…

022394a

…2.2.19 Bump rack from 2.2.18 to 2.2.19

eweitz added the build failure: false positive Build error confirmed as false positive. E.g. upstream service has a problem. label Oct 8, 2025

eweitz merged commit e84cc13 into main Oct 8, 2025
11 of 15 checks passed

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Release 1.103 #2309

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eweitz commented Oct 7, 2025

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eweitz commented Oct 8, 2025

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