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[Snyk] Upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.0 #343

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[Snyk] Upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.0 #343

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@jonkiky jonkiky commented Oct 1, 2024

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Snyk has created this PR to upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.0.

ℹ️ Keep your dependencies up-to-date. This makes it easier to fix existing vulnerabilities and to more quickly identify and fix newly disclosed vulnerabilities when they affect your project.

  • The recommended version is 8 versions ahead of your current version.

  • The recommended version was released on a month ago.

Release notes
Package name: @jbrowse/react-linear-genome-view
  • 2.15.0 - 2024-09-04

    This release has a couple updates

    • Update to MUIv6
    • Fix bug with BigBed names processing
    • Fix bug with e.g. @ jbrowse/react-linear-genome-view's view menu appearing incorrectly

    🚀 Enhancement

    • app-core, core, embedded-core, product-core, text-indexing, web-core

    🐛 Bug Fix

    • core, embedded-core
      • #4544 Fix cascading sub menus bug in embedded components in v2.14.0 (@ cmdcolin)
    • core
    • app-core

    Committers: 1

  • 2.14.0 - 2024-08-28

    This release adds some significant new features

    • Alignments track 'Group by' functionality: this features allows you to split an alignments track by a specific tag such as RG or HP into multiple new session tracks
    • A new adapter type to display sequence names from NCBI FASTA file such as NC_000001.10 in the user interface as chr1. This specifically targets the NCBI "sequence_report.tsv" format to do this renaming, and is called NcbiSequenceReportAliasAdapter

    image

    Example screenshot after applying the new Alignments track "Group by" functionality to group by the HP (haplotype) tag. Note that technically, each group is launched as a separate new "session track"

    🚀 Enhancement

    • core
      • #4532 De-duplicate snackbar messages (@ cmdcolin)
      • #4516 Add NCBI sequence_report.tsv alias adapter, with ability to recode NCBI fasta files to use UCSC style names (@ cmdcolin)
    • Other
      • #4533 Allow setting sequenceType='pep' in ReferenceSequenceTrack configuration (@ cmdcolin)
      • #4531 Add UnindexedFastaAdapter for fetching small plaintext FASTA files (@ cmdcolin)
      • #4528 Add description config slot to reference sequence track (@ cmdcolin)
    • app-core, core
    • core, product-core

    🐛 Bug Fix

    🏠 Internal

    • Other
      • #4530 Consolidate gff3 adapter featureData routine, avoid Number-ifying null phase (@ cmdcolin)
    • core
      • #4518 Don't send displayModel to "rendering" components on server side (@ cmdcolin)
    • __mocks__, app-core, core, embedded-core, product-core, text-indexing, web-core
      • #4513 Add new eslint rules (no-unnecessary-condition, no-unused-expressions, etc) and tsconfig noUncheckedIndexedAccess (@ cmdcolin)
    • app-core, core, embedded-core, product-core, text-indexing, web-core
    • core, product-core, text-indexing

    Committers: 2

  • 2.13.1 - 2024-07-31

    Fixes bug that caused the track selector in the linear synteny view to be unable to open in v2.13.0

    Also allows users to hide the track "outlines" in the linear genome view as an aesthetic preference

    without track outlines

    image

    with track outlines, and menu item to toggle it

    image

    🚀 Enhancement

    🐛 Bug Fix

    • #4501 Fix opening track selector in linear synteny view causing crash in v2.13.0 (@ cmdcolin)
    • #4495 Fix log scale for some types of signal tracks (@ cmdcolin)

    Committers: 1

  • 2.13.0 - 2024-07-25

    This release adds the ability to see the assembly name on each row of the synteny view, and adds a number of other small fixes

    image

    Example screenshot showing the assembly names on the far left for each row of a synteny view

    🚀 Enhancement

    🐛 Bug Fix

    • core
      • #4483 Fix configuration settings for track sorting in the track selector (@ cmdcolin)
    • Other
      • #4476 Fix config editor crash in vite usage of embedded components in dev mode (@ cmdcolin)
      • #4473 Fix 'Show no tracks active button' checkbox not working (@ cmdcolin)

    📝 Documentation

    🏠 Internal

    Committers: 3

  • 2.12.3 - 2024-06-27

    This is a hotfix release for a bug in desktop that affected v2.12.2 that prevented sessions from being started

    🚀 Enhancement

    • #4465 Add contig to the default dontRedispatch list for Gff3TabixAdapter (@ cmdcolin)
    • #4464 Bump generic-filehandle to put URL in error messages (@ cmdcolin)

    🐛 Bug Fix

    📝 Documentation

    • #4466 Add demo of using farm-fe bundler for embedded components (@ cmdcolin)

    Committers: 1

  • 2.12.2 - 2024-06-21

    This was a hotfix release to the v2.12.0 release to fix a Buffer is not defined error. See v2.12.0 release notes for more features https://github.com/GMOD/jbrowse-components/releases/v2.12.0

  • 2.12.1 - 2024-06-21

    v2.12.1

  • 2.12.0 - 2024-06-20

    This release includes

    • Added ability to show genomic or feature-relative coordinates in the "Show feature sequence" panel
    • Any sidebar widget can be popped out into a dialog box, allowing for more room to see the feature details, config editor, and more
    • Fixed sandbox error on startup of the linux AppImage on OSs with specific settings like Ubuntu 24
    • Added aggregation to BigBedAdapter for bigGenePred type tracks to make grouped gene glyphs (see screenshot)

    Before and after showing the aggregation of transcripts on a bigGenePred type track

    Example of the coordinates display on the feature sequence with the dialog

    🚀 Enhancement

    • Other
      • #4459 Allow using keyboard shortcut for devtools in production desktop builds (@ cmdcolin)
      • #4455 Add slot.type to configuration editor elements (@ cmdcolin)
      • #4427 Add ctrl+wheel scroll to zoom both top and bottom of synteny view (@ cmdcolin)
      • #4425 Add ability to dismiss dotplot warnings (@ cmdcolin)
      • #4422 Make initial linear synteny view import form submit show all regions by default (@ cmdcolin)
    • core
      • #4456 Add aggregation to BigBedAdapter to group bigGenePred transcripts (@ cmdcolin)
      • #4448 Adds genomic coordinates back into the sequence panel accounting for strand direction (@ carolinebridge)
      • #4423 Speed up large displayedRegions sets by converting MST array of Region[] into a types.frozen<IRegion[]> (@ cmdcolin)
      • #4399 Allow viewing coordinates in sequence feature display panel (@ cmdcolin)
    • app-core
      • #4443 Allow drawer widget to be "popped out" into a dialog box (@ cmdcolin)
    • core, product-core
      • #3992 Add ability to get refNames for a track in the "About track" panel (@ cmdcolin)

    🐛 Bug Fix

    • Other
      • #4458 Fix sandbox error on AppImage startup on certain linux systems (@ cmdcolin)
      • #4441 Fix sorting data grid on multi-wiggle 'Edit colors/arrangement' dialog (@ cmdcolin)
      • #4439 Fix blank lines in multi-wiggle add track workflow causing crash (@ cmdcolin)
      • #4438 Fix cursor:pointer style on an alignments feature detail clickable link (@ cmdcolin)
      • #4436 Fix "Open synteny view at this position" when file contains CIGAR X/= operators (@ cmdcolin)
      • #4426 Fix side scroll in linear synteny view causing the browser "back" action (@ cmdcolin)
      • #4417 Fix error message shown on chromosomes with missing data for plaintext GFF3 (@ cmdcolin)
    • core
      • #4442 Fix unstable dialog width in "About track" dialog for multi-quantitative tracks (@ cmdcolin)

    🏠 Internal

    Committers: 2

  • 2.11.2 - 2024-06-03

    This adds the ability for users and admins to configure filters to tracks. Users can edit the filters interactively with a "Edit filters" dialog box in the track menu, allowing them to only show features above a certain score, or of a certain type, etc.

    Screenshot showing the "Edit filters" dialog, making only a single feature type visible

    There is also an important bugfix for the "Show soft clipping" feature of alignments tracks

    🚀 Enhancement

    🐛 Bug Fix

    Committers: 3

from @jbrowse/react-linear-genome-view GitHub release notes

Important

  • Check the changes in this PR to ensure they won't cause issues with your project.
  • This PR was automatically created by Snyk using the credentials of a real user.

Note: You are seeing this because you or someone else with access to this repository has authorized Snyk to open upgrade PRs.

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fix: upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.0
a4eef7f 
Snyk has created this PR to upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.0.

See this package in npm:
@jbrowse/react-linear-genome-view

See this project in Snyk:
https://app.snyk.io/org/jonkiky/project/24b00042-56a8-40ef-ab6f-11e5db23e008?utm_source=github&utm_medium=referral&page=upgrade-pr
@sgvallala sgvallala closed this Oct 8, 2024
@sgvallala sgvallala deleted the snyk-upgrade-daf148f759f01e864b6b2a8f1056d6ad branch October 8, 2024 19:40
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@jonkiky @sgvallala @snyk-bot