Code

Revises Markdown Pages and Reports#19226

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Commits on Feb 13, 2025

• Add helper to generically split markdown sections without parsing arguments

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• Replace section parser in markdown component

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• Move argument resolution to markdown container

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• Add markdown renderer to default container

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• Move VegaWrapper to Common folder, use also in Markdown

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• Add vitessce wrapper template

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• Add plugin container

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• Add Vitessce to Markdown options?

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• Move visualization wrapper to visualizations

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• Fix naming for consistency

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• Move markdown galaxy section components to subdirectory

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• Convert Markdown main component to composition api

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• Adjust loading flag

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• Fix code editor props

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• Fix code editor handling

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• Restore text editor

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• Move text editor variant to separate component

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• Format client

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• Use markdown help modal within text editor component

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• Move help modal and buttons to parent wrapper

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• Refine markup

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• Allow switching between editor types

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• Add tooltip

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• Reduce editor font-size from 16 to 14

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• Resolve missing prop console warnings

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

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

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• Add event handler as prep to insert cells

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• Show arrow in popover

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• Add additional insert options

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• Consider editor layouts

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• Add ace editor

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• Refine code editor config

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• Align editor layout

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• Rename default section to markdown section

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• Map different modes to cell types

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• Add preliminary preview to markdown editor

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• Add update event handler to code cell

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• Add basic error handling to vega wrapper

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• Add error handling to shared vega wrapper

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• Show both, error message and previous preview

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• Move debounce handler into code cell

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• Add update handler to cell based markdown editor

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• Start drafting additional cell wrapper options

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• Adjust layout, switch to buttons

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• Add cell wrapper

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• Fix button alignment in cell editor guide column

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• Unify guide column buttons for now

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• Add toggle handler for code section

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• Add wrapper for guide buttons in cell editor

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• Add hover highlighting for cell wrapper

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• Do not irreversibly patch invocation markdown

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• Remove section mapper in workflow reports

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• Increase resilience of markdown provision to the front end

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• Add invocation_id to list of allowed arguments

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• Populate invocation identifier for inputs and ouputs containers

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• Restore invocation markdown handler

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

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• Remove unused helper function

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• Add Galaxy Wrapper to Cell Editor

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• Fix typescript, remove unused vars from license component

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• Remove unused regex expression in markdown utility for now

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• Add abstract placeholder functions for consistency

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• Update markdown utility comment for resolve_invocation_markdown procedure

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• Implement placeholders for relocated container types

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

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• Load invocation time without requiring pre populated invocation details

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• Remove invocations from markdown galaxy container

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• Convert markdown galaxy history link component to composition api

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

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• Remove histories from markdown galaxy container props

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• Fix post helper to import history from link

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

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• Remove time from markdown props

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• Make sure to trim before applying regex to match containers

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

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• Remove collections from galaxy container props

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• Convert collection display component to composition api

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• Improve visualization wrapper handling

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• Remove datasets prop from history dataset display component

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

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• Parse props individually to history dataset image component

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

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• Handle and add invocation data for invocation id in markdown

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• Move cell-guide to wrapper

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• Improve handling, display parsing errors

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• Use axios call for now, revisit invocation store later

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• Add step parser to markdown galaxy container

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• Add invocation input and output containers to markdown galaxy wrapper

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• Sort markdown galaxy container types alphabetically

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• Add implicit_collection_jobs_id to args if available

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• Add fallback case for already assigned target entries

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• Fix markdown container margins

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

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

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• Improve error handling in visualization wrapper

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• Generalize visualization wrapper

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• Refresh visualization on changes

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• Remove specialized visualization wrapper

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

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• Specify visualization wrapper height in styles

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• Add alert for invalid cell types

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• Add error handling to visualization wrapper

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• Add error message to output

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• Update ngl package version

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• Update ngl version

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• Add listener for posted messages

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• Add event handler to listen to galaxy charts form changes

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• Avoid redundant refresh, format json

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• Upgrade ngl version

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

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• Update charts package for plotly

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• Update to consistent message handler

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• Adjust config and title parsing

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• Add arrow buttons to cell guide

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• Align guide element styles

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• Fix popper for insert button

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• Add delete cell handler

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• Add on update handler

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• Allow cloning cells

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• Add handler to move cells up and down

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• Recreate code editor if cell type changes

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• Allow expanding when clicking on guide

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• Scroll to cloned or moved cell

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• Handle toggle state in cell editor

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• Disable move buttons when limits are reached

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• Add list for cell templates

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• Preliminary draft of insertion popover

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• Add basic templates

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• Fix scroll to new insert

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• Add basic template filter

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• Move filter helper to add button, simplify templates file

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

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• Add more draft entries to the insertion list

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• Remove unused = from template

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• Add placeholder configuration component to attach data

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• Align styles, add separator for config dialog

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

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• Move to subcomponent for data attachment

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• Update ngl and plotly packages with latest charts module

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• Close popover on escape

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

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• Use actual triangle for popper arrow

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• Update ngl and plotly package version

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

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• Draft data attachment select field

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• Improve error handling when selecting datasets, preserve dataset name

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• Remove unused import

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• Add ace code editor package

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• Adjust directive handler

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• Fix linting

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• Fix parse client test

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• Allow invocation identifier in custom report

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• Transition changes made in galaxyproject#19470 by @ahmedhamidawan

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• Fix unit tests

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• Fix invocation output unit test

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• Modularize data attachment selectors

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