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Merge 24.0 into 24.1#18239

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mvdbeek merged 85 commits intogalaxyproject:release_24.1galaxyproject/galaxy:release_24.1from mvdbeek:release_24.1mvdbeek/galaxy:release_24.1Copy head branch name to clipboardMay 28, 2024

+822-383

Commits

Commits on Mar 28, 2024

• do not expand datasets that are known to be inaccessible

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• include HDAInaccessible in AnyHDA union

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• reintroduce missing inaccessible state

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• fix a bug with using a supposedly optional caching key for a required operation

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• remove debug

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Commits on Mar 29, 2024

• prevent id conflict between hda and dataset

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• do not show storage selection to anons

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• Merge branch 'release_24.0' into noexpand-private

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• make inaccessible items non-draggable

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Commits on May 20, 2024

• Trigger redirct before rendering form

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• Fix undefined errors in ToolSucess component

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Commits on May 21, 2024

• Don't fail metadata if we only have an extra output files dir

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• Revert "Always create output"

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• Do not show the Edit UI when error accessing the dataset

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• Add client unit test for edit dataset error

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• Merge pull request galaxyproject#18187 from mvdbeek/fix_on_success_redirect

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• Create empty file if datatype is auto_primary_file

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• Create empty primary file if we only have extra files dir

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• Avoid object store path lookup when constructing JobState object

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• Merge pull request galaxyproject#18188 from davelopez/24.0_fix_edit_dataset_on_error

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• Move exit_code_file to fix AsynchronousJobState

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• Merge pull request galaxyproject#18190 from mvdbeek/fix_pulsar_async_update

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• Replace Multiselect selectLabel with icons in FormSelect

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Commits on May 22, 2024

• Raise appropriate API exceptions in history controller

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• Do not fail hard when one history fails to be made private

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• Allow to make private purged and archived histories

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• Drop redundant check after setting dataset permissions

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• Add selenium test that fails because wrong dataset is submitted

  mvdbeek

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• Fix Select value prop type

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• Also filter out matchedValues using tags

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• Remove unnecessary catch all

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• Merge pull request galaxyproject#18200 from davelopez/24.0_fix_make_private_immutable

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• fix jests since each option is in a div instead of a span

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• [24.0] Prevent anonymous users from running workflows

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• add api test for running workflow as anon user

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• Remove legacy ref to sqlalchemy migrate

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• [24.0] Add GenericItem error handling

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• Merge pull request galaxyproject#18202 from jdavcs/240_ts_db_script

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Commits on May 23, 2024

• Add string cast for dbkey / genome_build

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• Include stack when reporting delete error

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• Merge pull request galaxyproject#18193 from mvdbeek/fix_tag_filter_workflow_run_form

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• Merge pull request galaxyproject#18207 from mvdbeek/fix_genome_build_int

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• Merge pull request galaxyproject#18208 from mvdbeek/exc_info_in_object_store_delete

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• Merge pull request galaxyproject#18194 from ahmedhamidawan/replace_multiselect_label_with_icon

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• Limit templated visualization data, fix PCA plot for tabular datasets

  mvdbeek

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• Fix display of error messages in visualizations

  mvdbeek

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• Merge pull request galaxyproject#18211 from mvdbeek/fix_pca_3d_rendering_and_error_handling

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• Merge pull request galaxyproject#18179 from mvdbeek/fix_extra_files_dir_only_collection_pulsar

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• Use job permissions instead of token

  nsoranzo

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• Update versions of GitHub actions

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• Use official minikube GitHub action

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• Update syntax for labeler action v5

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• Exclude bcsl.ts test files from CodeQL code scanning

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• add titles to Toasts for GenericItem

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• Update client/src/components/History/Content/GenericItem.vue

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• Update lib/galaxy/webapps/galaxy/services/workflows.py

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• Check dataset state when attempting to acces dataset contents

  mvdbeek

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• Merge pull request galaxyproject#18203 from ahmedhamidawan/fix_content_item_on_error

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• Use config_section to distinguish between galaxy and ts or other apps

  jdavcs

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• Merge pull request galaxyproject#18212 from nsoranzo/release_24.0_backport_18197

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• Merge pull request galaxyproject#18215 from jdavcs/240_ts_db_script

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• Restrict job_files access to jobs that are not terminal

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• Merge pull request galaxyproject#18192 from ahmedhamidawan/prevent_anon_users_run_workflow

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Commits on May 24, 2024

• Merge pull request galaxyproject#18217 from mvdbeek/tighten_job_access

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• Fix bool const OpenAPI TS schema conversion

  davelopez

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• Serialize accessible field for collection elements

  davelopez

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• Add missing event declaration

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• Avoid requesting details for inaccessible datasets

  davelopez

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• Make accessible optional in HDAObject

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• Merge pull request galaxyproject#18214 from mvdbeek/error_messages_when_accessing_datasets_we_cannot_access

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• Raise appropriate exception if accessing deleted input file

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Commits on May 25, 2024

• Merge pull request galaxyproject#17818 from martenson/noexpand-private

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Commits on May 27, 2024

• Decrease visualization log level

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• Raise RequestParameterInvalidException if url can't be verified

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• Don't set dataset peek for errored jobs

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• Refactor set_peek and move exception handling

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• Don't fail set_peek if file does not look like GRO file

  mvdbeek

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• Reset content-length for unhandled exceptions

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• Merge pull request galaxyproject#18230 from mvdbeek/exception_handling_fetch_invalid_url

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• Merge pull request galaxyproject#18231 from mvdbeek/set_peek_on_success_only

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• Merge pull request galaxyproject#18229 from mvdbeek/decrease_visualization_log_level

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• Merge pull request galaxyproject#18223 from mvdbeek/discriminate_inputs_deleted_job_files

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• Merge pull request galaxyproject#18233 from mvdbeek/reset_content_length_if_no_error_handling

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Commits on May 28, 2024

• Merge branch 'release_24.0' into release_24.1

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• Fix up loading failed error state in Dataset Attributes component

  mvdbeek

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