Code

Revises Markdown Pages and Reports#19226

Code

Draft

guerler wants to merge 156 commits intogalaxyproject:devgalaxyproject/galaxy:devfrom guerler:reports_revisionguerler/galaxy:reports_revisionCopy head branch name to clipboard

+2,538-1,248

Commits

Commits on Feb 7, 2025

• Add helper to generically split markdown sections without parsing arguments

  guerler

  committed
  04527ec

  Copy full SHA for 04527ec

• Replace section parser in markdown component

  guerler

  committed
  fe64a01

  Copy full SHA for fe64a01

• Move argument resolution to markdown container

  guerler

  committed
  89f3877

  Copy full SHA for 89f3877

• Add markdown renderer to default container

  guerler

  committed
  152066c

  Copy full SHA for 152066c

• Move VegaWrapper to Common folder, use also in Markdown

  guerler

  committed
  0d266cc

  Copy full SHA for 0d266cc

• Add vitessce wrapper template

  guerler

  committed
  db0c375

  Copy full SHA for db0c375

• Add plugin container

  guerler

  committed
  5fc39e1

  Copy full SHA for 5fc39e1

• Add Vitessce to Markdown options?

  guerler

  committed
  7691b63

  Copy full SHA for 7691b63

• Move visualization wrapper to visualizations

  guerler

  committed
  68ff340

  Copy full SHA for 68ff340

• Fix naming for consistency

  guerler

  committed
  9b70305

  Copy full SHA for 9b70305

• Move markdown galaxy section components to subdirectory

  guerler

  committed
  44b49a3

  Copy full SHA for 44b49a3

• Convert Markdown main component to composition api

  guerler

  committed
  3fb0449

  Copy full SHA for 3fb0449

• Adjust loading flag

  guerler

  committed
  263b753

  Copy full SHA for 263b753

• Fix code editor props

  guerler

  committed
  9a5b2d0

  Copy full SHA for 9a5b2d0

• Fix code editor handling

  guerler

  committed
  f93a443

  Copy full SHA for f93a443

• Restore text editor

  guerler

  committed
  e41a263

  Copy full SHA for e41a263

• Move text editor variant to separate component

  guerler

  committed
  180b6ed

  Copy full SHA for 180b6ed

• Format client

  guerler

  committed
  202bf04

  Copy full SHA for 202bf04

• Use markdown help modal within text editor component

  guerler

  committed
  0d3f3d7

  Copy full SHA for 0d3f3d7

• Move help modal and buttons to parent wrapper

  guerler

  committed
  b4a0c60

  Copy full SHA for b4a0c60

• Refine markup

  guerler

  committed
  f6a4efb

  Copy full SHA for f6a4efb

• Allow switching between editor types

  guerler

  committed
  852a886

  Copy full SHA for 852a886

• Add tooltip

  guerler

  committed
  26dbefe

  Copy full SHA for 26dbefe

• Reduce editor font-size from 16 to 14

  guerler

  committed
  e156449

  Copy full SHA for e156449

• Resolve missing prop console warnings

  guerler

  committed
  5fa81a4

  Copy full SHA for 5fa81a4

• Avoid parsing empty rows, prepare for more generalized typing in parse module

  guerler

  committed
  b0b7d87

  Copy full SHA for b0b7d87

• Use documented option to place popper instead of manually applying margin

  guerler

  committed
  f4f1169

  Copy full SHA for f4f1169

• Add event handler as prep to insert cells

  guerler

  committed
  94b277c

  Copy full SHA for 94b277c

• Show arrow in popover

  guerler

  committed
  ba57c60

  Copy full SHA for ba57c60

• Add additional insert options

  guerler

  committed
  6b49a2d

  Copy full SHA for 6b49a2d

• Consider editor layouts

  guerler

  committed
  0337f2f

  Copy full SHA for 0337f2f

• Add ace editor

  guerler

  committed
  ef41008

  Copy full SHA for ef41008

• Refine code editor config

  guerler

  committed
  c36ecb3

  Copy full SHA for c36ecb3

• Align editor layout

  guerler

  committed
  bed385f

  Copy full SHA for bed385f

• Rename default section to markdown section

  guerler

  committed
  9945281

  Copy full SHA for 9945281

• Map different modes to cell types

  guerler

  committed
  627ff9c

  Copy full SHA for 627ff9c

• Add preliminary preview to markdown editor

  guerler

  committed
  2e7fa6e

  Copy full SHA for 2e7fa6e

• Add update event handler to code cell

  guerler

  committed
  e5a302c

  Copy full SHA for e5a302c

• Add basic error handling to vega wrapper

  guerler

  committed
  a4cacd5

  Copy full SHA for a4cacd5

• Add error handling to shared vega wrapper

  guerler

  committed
  b0af9fd

  Copy full SHA for b0af9fd

• Show both, error message and previous preview

  guerler

  committed
  38fcc29

  Copy full SHA for 38fcc29

• Move debounce handler into code cell

  guerler

  committed
  2e1325a

  Copy full SHA for 2e1325a

• Add update handler to cell based markdown editor

  guerler

  committed
  28e4371

  Copy full SHA for 28e4371

• Start drafting additional cell wrapper options

  guerler

  committed
  c1e7092

  Copy full SHA for c1e7092

• Adjust layout, switch to buttons

  guerler

  committed
  e37809f

  Copy full SHA for e37809f

• Add cell wrapper

  guerler

  committed
  8912aeb

  Copy full SHA for 8912aeb

• Fix button alignment in cell editor guide column

  guerler

  committed
  acfb196

  Copy full SHA for acfb196

• Unify guide column buttons for now

  guerler

  committed
  10ae825

  Copy full SHA for 10ae825

• Add toggle handler for code section

  guerler

  committed
  9ad3120

  Copy full SHA for 9ad3120

• Add wrapper for guide buttons in cell editor

  guerler

  committed
  b660d24

  Copy full SHA for b660d24

• Add hover highlighting for cell wrapper

  guerler

  committed
  002221c

  Copy full SHA for 002221c

• Do not irreversibly patch invocation markdown

  guerler

  committed
  960bc68

  Copy full SHA for 960bc68

• Remove section mapper in workflow reports

  guerler

  committed
  249d516

  Copy full SHA for 249d516

• Increase resilience of markdown provision to the front end

  guerler

  committed
  8f343fb

  Copy full SHA for 8f343fb

• Add invocation_id to list of allowed arguments

  guerler

  committed
  9847b08

  Copy full SHA for 9847b08

• Populate invocation identifier for inputs and ouputs containers

  guerler

  committed
  e9ef756

  Copy full SHA for e9ef756

• Restore invocation markdown handler

  guerler

  committed
  adcf92c

  Copy full SHA for adcf92c

• Add invocation id to to entries containing input, output or step attributes

  guerler

  committed
  0d8be3e

  Copy full SHA for 0d8be3e

• Remove unused helper function

  guerler

  committed
  0ecda3d

  Copy full SHA for 0ecda3d

• Add Galaxy Wrapper to Cell Editor

  guerler

  committed
  217a92e

  Copy full SHA for 217a92e

• Fix typescript, remove unused vars from license component

  guerler

  committed
  e59d919

  Copy full SHA for e59d919

• Remove unused regex expression in markdown utility for now

  guerler

  committed
  177a1fd

  Copy full SHA for 177a1fd

• Add abstract placeholder functions for consistency

  guerler

  committed
  943cdbd

  Copy full SHA for 943cdbd

• Update markdown utility comment for resolve_invocation_markdown procedure

  guerler

  committed
  1426bbd

  Copy full SHA for 1426bbd

• Implement placeholders for relocated container types

  guerler

  committed
  5316a82

  Copy full SHA for 5316a82

• Remove prepopulated workflows list from markdown wrapper, use axios for now since store is not available

  guerler

  committed
  9212714

  Copy full SHA for 9212714

• Load invocation time without requiring pre populated invocation details

  guerler

  committed
  e59ad9e

  Copy full SHA for e59ad9e

• Remove invocations from markdown galaxy container

  guerler

  committed
  38b2e6f

  Copy full SHA for 38b2e6f

• Convert markdown galaxy history link component to composition api

  guerler

  committed
  dfcd89b

  Copy full SHA for dfcd89b

• Decouple history link from requiring prepopulated history summaries, should use stores

  guerler

  committed
  ff9ab9a

  Copy full SHA for ff9ab9a

• Remove histories from markdown galaxy container props

  guerler

  committed
  888c434

  Copy full SHA for 888c434

• Fix post helper to import history from link

  guerler

  committed
  93c98fe

  Copy full SHA for 93c98fe

• Remove version major prop from markdown component, version is already avaiable in instance data

  guerler

  committed
  d48cd0b

  Copy full SHA for d48cd0b

• Remove time from markdown props

  guerler

  committed
  d8c1af8

  Copy full SHA for d8c1af8

• Make sure to trim before applying regex to match containers

  guerler

  committed
  9b882de

  Copy full SHA for 9b882de

• Avoid using prepopulated collection details to access name in collection display component

  guerler

  committed
  d4eb070

  Copy full SHA for d4eb070

• Remove collections from galaxy container props

  guerler

  committed
  83386fe

  Copy full SHA for 83386fe

• Convert collection display component to composition api

  guerler

  committed
  e6cbd85

  Copy full SHA for e6cbd85

• Improve visualization wrapper handling

  guerler

  committed
  bdeba3b

  Copy full SHA for bdeba3b

• Remove datasets prop from history dataset display component

  guerler

  committed
  7ea5da6

  Copy full SHA for 7ea5da6

• Obtain dataset name and type from metadata url provider in dataset display component

  guerler

  committed
  70b4653

  Copy full SHA for 70b4653

• Parse props individually to history dataset image component

  guerler

  committed
  e4816dd

  Copy full SHA for e4816dd

• Convert history dataset details and display components to composition api, remove prepopulated datasets props

  guerler

  committed
  ab32328

  Copy full SHA for ab32328

• Handle and add invocation data for invocation id in markdown

  guerler

  committed
  55ba108

  Copy full SHA for 55ba108

• Move cell-guide to wrapper

  guerler

  committed
  4354ec8

  Copy full SHA for 4354ec8

• Improve handling, display parsing errors

  guerler

  committed
  fe941b6

  Copy full SHA for fe941b6

• Use axios call for now, revisit invocation store later

  guerler

  committed
  58e26e4

  Copy full SHA for 58e26e4

• Add step parser to markdown galaxy container

  guerler

  committed
  8dcc99b

  Copy full SHA for 8dcc99b

• Add invocation input and output containers to markdown galaxy wrapper

  guerler

  committed
  d647c7f

  Copy full SHA for d647c7f

• Sort markdown galaxy container types alphabetically

  guerler

  committed
  04485df

  Copy full SHA for 04485df

• Add implicit_collection_jobs_id to args if available

  guerler

  committed
  ef8ef9b

  Copy full SHA for ef8ef9b

• Add fallback case for already assigned target entries

  guerler

  committed
  015261a

  Copy full SHA for 015261a

• Fix markdown container margins

  guerler

  committed
  9dff093

  Copy full SHA for 9dff093

• Use simple caching to avoid duplicate requests on markdown page loading for now, improve error handling in history link component

  guerler

  committed
  c774589

  Copy full SHA for c774589

• Collect plugin data from api instead of relying on static path sources

  guerler

  committed
  b7bc2bc

  Copy full SHA for b7bc2bc

• Improve error handling in visualization wrapper

  guerler

  committed
  2107c31

  Copy full SHA for 2107c31

• Generalize visualization wrapper

  guerler

  committed
  ba9a8bf

  Copy full SHA for ba9a8bf

• Refresh visualization on changes

  guerler

  committed
  3ba4d57

  Copy full SHA for 3ba4d57

• Remove specialized visualization wrapper

  guerler

  committed
  d99e67a

  Copy full SHA for d99e67a

• Adjust size, ensure that error message does not resize view

  guerler

  committed
  b9942a1

  Copy full SHA for b9942a1

• Specify visualization wrapper height in styles

  guerler

  committed
  3aaecd1

  Copy full SHA for 3aaecd1

• Add alert for invalid cell types

  guerler

  committed
  93e9ff2

  Copy full SHA for 93e9ff2

• Add error handling to visualization wrapper

  guerler

  committed
  0e1aae3

  Copy full SHA for 0e1aae3

• Add error message to output

  guerler

  committed
  efe9151

  Copy full SHA for efe9151

• Update ngl package version

  guerler

  committed
  e8c97d5

  Copy full SHA for e8c97d5

• Update ngl version

  guerler

  committed
  66bfb59

  Copy full SHA for 66bfb59

• Add listener for posted messages

  guerler

  committed
  319cdaf

  Copy full SHA for 319cdaf

• Add event handler to listen to galaxy charts form changes

  guerler

  committed
  251328a

  Copy full SHA for 251328a

• Avoid redundant refresh, format json

  guerler

  committed
  16b59ab

  Copy full SHA for 16b59ab

• Upgrade ngl version

  guerler

  committed
  6a74155

  Copy full SHA for 6a74155

• Access posted message using generic source name, parse object directly

  guerler

  committed
  7e01aea

  Copy full SHA for 7e01aea

• Update charts package for plotly

  guerler

  committed
  1430797

  Copy full SHA for 1430797

• Update to consistent message handler

  guerler

  committed
  423fe2c

  Copy full SHA for 423fe2c

• Adjust config and title parsing

  guerler

  committed
  1632e74

  Copy full SHA for 1632e74

• Add arrow buttons to cell guide

  guerler

  committed
  33a85f2

  Copy full SHA for 33a85f2

• Align guide element styles

  guerler

  committed
  1211637

  Copy full SHA for 1211637

• Fix popper for insert button

  guerler

  committed
  f4a8510

  Copy full SHA for f4a8510

• Add delete cell handler

  guerler

  committed
  8171f62

  Copy full SHA for 8171f62

• Add on update handler

  guerler

  committed
  b1754e9

  Copy full SHA for b1754e9

• Allow cloning cells

  guerler

  committed
  a30f866

  Copy full SHA for a30f866

• Add handler to move cells up and down

  guerler

  committed
  f8b4550

  Copy full SHA for f8b4550

• Recreate code editor if cell type changes

  guerler

  committed
  39f773b

  Copy full SHA for 39f773b

• Allow expanding when clicking on guide

  guerler

  committed
  b02cd6b

  Copy full SHA for b02cd6b

• Scroll to cloned or moved cell

  guerler

  committed
  7f649c8

  Copy full SHA for 7f649c8

• Handle toggle state in cell editor

  guerler

  committed
  5188b4f

  Copy full SHA for 5188b4f

• Disable move buttons when limits are reached

  guerler

  committed
  913e41b

  Copy full SHA for 913e41b

• Add list for cell templates

  guerler

  committed
  27d36b1

  Copy full SHA for 27d36b1

• Preliminary draft of insertion popover

  guerler

  committed
  0ae5a1e

  Copy full SHA for 0ae5a1e

• Add basic templates

  guerler

  committed
  ba8648b

  Copy full SHA for ba8648b

• Fix scroll to new insert

  guerler

  committed
  6af167a

  Copy full SHA for 6af167a

• Add basic template filter

  guerler

  committed
  f85a6de

  Copy full SHA for f85a6de

• Move filter helper to add button, simplify templates file

  guerler

  committed
  68aeb8c

  Copy full SHA for 68aeb8c

• Add error message if filtering fails, fix popup closing on background

  guerler

  committed
  992b17f

  Copy full SHA for 992b17f

• Add more draft entries to the insertion list

  guerler

  committed
  e83aa93

  Copy full SHA for e83aa93

• Remove unused = from template

  guerler

  committed
  cbfa6da

  Copy full SHA for cbfa6da

• Add placeholder configuration component to attach data

  guerler

  committed
  0e602a8

  Copy full SHA for 0e602a8

• Align styles, add separator for config dialog

  guerler

  committed
  1e365f6

  Copy full SHA for 1e365f6

• Add close event handlers for data attachment view, hide option for markdown cells

  guerler

  committed
  f1f8566

  Copy full SHA for f1f8566

• Move to subcomponent for data attachment

  guerler

  committed
  a314601

  Copy full SHA for a314601

• Update ngl and plotly packages with latest charts module

  guerler

  committed
  74ac42c

  Copy full SHA for 74ac42c

• Close popover on escape

  guerler

  committed
  e7eaa01

  Copy full SHA for e7eaa01

• Add additional option to close when clicking on particular elements inside the popup, simplify disabled prop handling

  guerler

  committed
  7896505

  Copy full SHA for 7896505

• Use actual triangle for popper arrow

  guerler

  committed
  755e15d

  Copy full SHA for 755e15d

• Update ngl and plotly package version

  guerler

  committed
  3f1593a

  Copy full SHA for 3f1593a

Commits on Feb 8, 2025

• Update charts package with fixed tooltip attachment, add warning to data attachment component

  guerler

  committed
  1e5afef

  Copy full SHA for 1e5afef

• Draft data attachment select field

  guerler

  committed
  2ea5cf4

  Copy full SHA for 2ea5cf4

• Improve error handling when selecting datasets, preserve dataset name

  guerler

  committed
  eabe088

  Copy full SHA for eabe088

• Remove unused import

  guerler

  committed
  70122c1

  Copy full SHA for 70122c1

• Add ace code editor package

  guerler

  committed
  3acbc4b

  Copy full SHA for 3acbc4b

Commits on Feb 9, 2025

• Adjust directive handler

  guerler

  committed
  ce21270

  Copy full SHA for ce21270

• Fix linting

  guerler

  committed
  371c722

  Copy full SHA for 371c722

• Fix parse client test

  guerler

  committed
  62157fe

  Copy full SHA for 62157fe

• Allow invocation identifier in custom report

  guerler

  committed
  cd4648c

  Copy full SHA for cd4648c

• Transition changes made in galaxyproject#19470 by @ahmedhamidawan

  guerler

  committed
  728c3f7

  Copy full SHA for 728c3f7

Commits on Feb 10, 2025

• Fix unit tests

  guerler

  committed
  9bf6fc0

  Copy full SHA for 9bf6fc0

• Fix invocation output unit test

  guerler

  committed
  e5bcb5b

  Copy full SHA for e5bcb5b