Code

Merge release_23.0 into dev#16088

Code

Merged

davelopez merged 104 commits intogalaxyproject:devgalaxyproject/galaxy:devfrom nsoranzo:merge_release_23.0_20230513nsoranzo/galaxy:merge_release_23.0_20230513Copy head branch name to clipboardMay 15, 2023

+1,524-739

Commits

Commits on Mar 30, 2023

• fix assertion linters

  Show description for a15fd1f
  bernt-matthias

  committed
  a15fd1f

• fix type annotations for assertions

  Show description for 566a87d
  bernt-matthias

  committed
  566a87d

• assertion typing: allow int/bool in addition to str

  bernt-matthias

  committed
  fd7963b

Commits on Apr 20, 2023

• Handle empty lines better in tabular display dataset parsing

  dannon

  committed
  ed7c2d6

• Expand last column to fill tabular display table for better formatting

  dannon

  committed
  c6067f7

Commits on Apr 25, 2023

• Display history name

  Show description for 2328939
  davelopez

  committed
  2328939

• Expose 'prepare only' actions for STS composable

  Show description for 385f154
  davelopez

  committed
  385f154

• Make direct downloads more obvious

  Show description for 18891fd
  davelopez

  committed
  18891fd

Commits on Apr 26, 2023

• Merge pull request galaxyproject#15991 from davelopez/23.0_fix_history_export_papercuts

  Show description for 85df98a
  dannon

  authored
  85df98a

• Reset the selection after building a collection

  Show description for 029a27d
  davelopez

  committed
  029a27d

• Clarify search behavior in placeholder text

  Show description for 4dda1b5
  davelopez

  committed
  4dda1b5

• Improve display chunk generation for BAMs

  Show description for 7229cf0
  

  wm75

  authored and

  mvdbeek

  committed
  7229cf0

• Fix wrongly saved file

  

  wm75

  authored and

  mvdbeek

  committed
  65c16ab

• Fix linting

  

  wm75

  authored and

  mvdbeek

  committed
  e6c7c2b

• Merge pull request galaxyproject#16005 from davelopez/23.0_fix_history_items_selector

  Show description for 18cb605
  dannon

  authored
  18cb605

Commits on Apr 27, 2023

• Remove no longer valid TODO comment

  Show description for e178967
  davelopez

  committed
  e178967

• Merge pull request galaxyproject#16007 from mvdbeek/backport_bam_fix

  Show description for d1cf060
  dannon

  authored
  d1cf060

• Add test case for missing dataset file

  davelopez

  committed
  6ec4020

• Rename add_dataset to include_dataset_file

  Show description for 6c53512
  davelopez

  committed
  6c53512

• Allow setting auto_decompress property in staging interface

  Show description for a41a098
  mvdbeek

  committed
  a41a098

Commits on Apr 28, 2023

• Merge pull request galaxyproject#16014 from mvdbeek/add_decompress_flag_to_staging_code

  Show description for 23628cb
  martenson

  authored
  23628cb

• Merge pull request galaxyproject#16006 from davelopez/23.0_fix_missleading_placeholder_text_pub_histories

  Show description for 22f3545
  martenson

  authored
  22f3545

• convert WorkflowEdges to canvas

  Show description for 2c9f235
  ElectronicBlueberry

  committed
  2c9f235

• refactor Connection to interface

  Show description for 83a368d
  ElectronicBlueberry

  committed
  83a368d

• make node position relative

  Show description for 3529c79
  ElectronicBlueberry

  committed
  3529c79

• more granular reactivity

  Show description for 279a8d8
  ElectronicBlueberry

  committed
  279a8d8

• use more strict implementation of pushOrSet

  Show description for fa6d691
  ElectronicBlueberry

  committed
  fa6d691

• remove unused css

  ElectronicBlueberry

  committed
  b095721

• convert connections to svg

  ElectronicBlueberry

  committed
  81ecce1

• add tsconfig tweak to stop dev server crashes

  ElectronicBlueberry

  committed
  ba556c7

• fix initial rendering of edges

  ElectronicBlueberry

  committed
  1e623fc

• remove drawable connection composable

  ElectronicBlueberry

  committed
  72cbea9

• undo test noop

  ElectronicBlueberry

  committed
  09a5297

• restore navigation.yml

  ElectronicBlueberry

  committed
  9dc6816

• rename connection

  Show description for ce67102
  ElectronicBlueberry

  committed
  ce67102

• fix connection drop

  ElectronicBlueberry

  committed
  c228da4

• fix initial loading of invalid connections

  ElectronicBlueberry

  committed
  a2ff1e9

• Ensure a dataset in OK state has a valid file

  Show description for ab03bb0
  davelopez

  committed
  ab03bb0

• Shortcut condition to avoid checking the disk

  Show description for 649e056
  davelopez

  committed
  649e056

• Use better name

  Show description for c616c6e
  

  davelopez

  and

  mvdbeek

  authored
  c616c6e

• Fix condition

  Show description for af5b244
  

  davelopez

  and

  mvdbeek

  authored
  af5b244

• Fix reports graphs; use secondary version of d3v3 for compat

  dannon

  committed
  69a5272

• Fix reports masthead

  dannon

  committed
  57c1bd8

• Load sparkline in jquery.custom -- used in reports, drop after we either

  Show description for c9b794e
  dannon

  committed
  c9b794e

Commits on May 1, 2023

• Make Expression Tools searchable in ToolBoxWorkflow

  ahmedhamidawan

  committed
  6cb911e

Commits on May 2, 2023

• Add support for auto-importing workflows via Tutorial Mode

  

  hexylena

  authored and

  dannon

  committed
  e7b533d

• Add very basic tutorial mode test case

  

  hexylena

  authored and

  dannon

  committed
  f0b52d8

• Adjust trs url handle, and path pushed

  dannon

  committed
  15b5977

• Apply suggestions from code review

  Show description for ecb37f7
  

  dannon

  and

  hexylena

  committed
  ecb37f7

• Fix up test imports, formatting.

  dannon

  committed
  81a2e24

• Log object store id too

  davelopez

  committed
  36bfae1

• Variable safety

  dannon

  committed
  e72edc3

• Minor tweak to keydown listener, format

  dannon

  committed
  dea5f3e

• make uri_prefixes stricter

  

  ElectronicBlueberry

  authored and

  mvdbeek

  committed
  4afd469

• Merge pull request galaxyproject#16022 from ahmedhamidawan/expression_tools_search

  Show description for 8ef3518
  mvdbeek

  authored
  8ef3518

• Fix galaxy proxy active style on body

  dannon

  committed
  9dad4ac

• Fix click event binding; this was broken when swapping away from jquery -- click() is not vanilla js

  dannon

  committed
  706dda2

• Drop unused restoreLocation

  dannon

  committed
  3078b8d

• Merge pull request galaxyproject#16015 from dannon/fix-reports

  Show description for 89cb7ca
  mvdbeek

  authored
  89cb7ca

• Merge pull request galaxyproject#16000 from ElectronicBlueberry/workflow-connections-performance-svg

  Show description for 82694e6
  mvdbeek

  authored
  82694e6

• Merge pull request galaxyproject#15970 from dannon/tabular-view-fixes

  Show description for 2bc34c5
  mvdbeek

  authored
  2bc34c5

• Redo workflow element handling

  dannon

  committed
  36bebd2

• Include more dataset info on error

  Show description for 1d02485
  

  davelopez

  and

  mvdbeek

  committed
  1d02485

• Merge pull request galaxyproject#16024 from mvdbeek/file-paste-backport

  Show description for ec1cf86
  dannon

  authored
  ec1cf86

• Refactor test to assert for specific error

  davelopez

  committed
  7f5e97a

• Merge pull request galaxyproject#16013 from davelopez/23.0_ensure_history_export_contains_all_datasets

  Show description for 6f4d891
  mvdbeek

  authored
  6f4d891

Commits on May 3, 2023

• Fix leftover jquery style class change

  hexylena

  committed
  096ed7b

• Merge pull request galaxyproject#15684 from hexylena/gtn-trs

  Show description for 0aff863
  dannon

  authored
  0aff863

Commits on May 4, 2023

• Fix vscode test discovery, noisy startup logs, set_meta stderr

  Show description for f488d9f
  mvdbeek

  committed
  f488d9f

• Merge pull request galaxyproject#16039 from mvdbeek/fix_gcsfs_test_discovery

  Show description for 1811f6d
  mvdbeek

  authored
  1811f6d

• Install node from setup-node action in more tests

  Show description for 3a2e936
  mvdbeek

  committed
  3a2e936

• Replace httpbin service with pytest-httpserver

  Show description for d2271e5
  mvdbeek

  committed
  d2271e5

• Replace httpbin service with pytest-httpserver

  Show description for 69ebbb7
  mvdbeek

  committed
  69ebbb7

• Merge pull request galaxyproject#16043 from mvdbeek/install_node_from_github_action

  Show description for 387b083
  dannon

  authored
  387b083

• Merge pull request galaxyproject#16042 from mvdbeek/replace_httpbin

  Show description for 7a9ba0c
  martenson

  authored
  7a9ba0c

Commits on May 5, 2023

• Add test case for name-contains query on histories

  davelopez

  committed
  fa35e52

• Fix case insensitive orm filtering in lists

  Show description for 417029d
  davelopez

  committed
  417029d

• Merge pull request galaxyproject#16036 from davelopez/23.0_fix_case_sensitive_filtering

  Show description for cc2e8a8
  bgruening

  authored
  cc2e8a8

• Update pulsar to 0.15.2

  Show description for 81b42f0
  mvdbeek

  committed
  81b42f0

• Various fixes to path prefix handling

  Show description for d5ab296
  mvdbeek

  committed
  d5ab296

• Merge pull request galaxyproject#16033 from mvdbeek/path_prefix_handling

  Show description for a9428a1
  dannon

  authored
  a9428a1

Commits on May 6, 2023

• Merge pull request galaxyproject#16050 from mvdbeek/pulsar_update_0_15_2

  Show description for 65bb4e4
  mvdbeek

  authored
  65bb4e4

• Fix minor error in WorkflowList help modal

  ahmedhamidawan

  committed
  1484237

Commits on May 8, 2023

• Fix for missing Href to Composables pass-through component

  

  hujambo-dunia

  authored and

  davelopez

  committed
  63df9be

• Fix for link pop-up window/toaster after Data Library to History import

  

  hujambo-dunia

  authored and

  davelopez

  committed
  873a433

• Update client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js

  Show description for 9da3b03
  

  2 peopleauthored and

  davelopez

  committed
  9da3b03

• Merge pull request galaxyproject#16057 from ahmedhamidawan/workflows_info_modal_is_shared

  Show description for 74eb844
  davelopez

  authored
  74eb844

• Merge pull request galaxyproject#16060 from davelopez/23.0_backport_#16008

  Show description for 7421240
  martenson

  authored
  7421240

Commits on May 9, 2023

• Display DCE in job parameter component

  Show description for ac432a5
  mvdbeek

  committed
  ac432a5

• Wait for tool form data to be set before refreshing tool form

  Show description for 13514a7
  mvdbeek

  committed
  13514a7

• Fix re-run with DCE inputs

  mvdbeek

  committed
  c14db55

• Merge pull request galaxyproject#15873 from bernt-matthias/topic/fix-assertion-bytes

  Show description for 012102d
  mvdbeek

  authored
  012102d

• Also patch values when setting list of selected datasets

  mvdbeek

  committed
  668c2ed

• Anonymous User tool link bug fix

  Show description for a9911be
  ahmedhamidawan

  committed
  a9911be

Commits on May 10, 2023

• Merge pull request galaxyproject#16065 from ahmedhamidawan/tool_link_share_anon

  Show description for f856207
  davelopez

  authored
  f856207

• Don't build tool state for first param combination

  Show description for b9bb92c
  mvdbeek

  committed
  b9bb92c

• Selemium test for re-running part of dataset collection via DCE

  mvdbeek

  committed
  3ce0a8d

Commits on May 11, 2023

• Merge pull request galaxyproject#15744 from mvdbeek/dce_display

  Show description for 5ec64b9
  dannon

  authored
  5ec64b9

• Merge branch 'release_22.05' into release_23.0

  nsoranzo

  committed
  19e361b

Commits on May 12, 2023

• Fix BCO export by updating gxformat2

  Show description for 4d6008f
  mvdbeek

  committed
  4d6008f

• Merge pull request galaxyproject#16081 from mvdbeek/gxformat2_update

  Show description for a4266b8
  martenson

  authored
  a4266b8

Commits on May 14, 2023

• Merge branch 'release_23.0' into dev

  nsoranzo

  committed
  ab99721

• Partially fix merge forward for HistoryExport

  Show description for 16be4b6
  

  davelopez

  authored and

  nsoranzo

  committed
  16be4b6

Commits on May 15, 2023

• fix computed getter mock in HistoryExport test

  ElectronicBlueberry

  committed
  e93729f