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CHANGELOG.md

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GeneNoteBook Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning

Unreleased

Added

  • User accounts can be added/changed/removed from the CLI
  • Bulk operations for user account management through CLI
  • --dbStartupTimeout option to genenotebook run to allow specifying how long to wait for the mongo daemon to start
  • --dbCacheSizeGB option to genenotebook run to allow specifying how many GBs of RAM can be used for mongodb cache.

Changed

  • Removed settings.json
  • Phylogenetic tree now made with react-bio-viz
  • Meteor version 2.5.6

Fixed

  • Once again fixed version display
  • Popover menus

[0.3.0] 2021-09-17

Added

  • External links and descriptions on GO terms and INTERPRO ids
  • Make the list of default user accounts configurable using settings.json configuration file
  • Ability to upload genome sequence through the browser

Changed

  • Meteor version 2.4
  • Node.js version 14

Fixed

  • Option parsing for CLI
  • Version display in browser

0.2.0 2020-01-22

Added

  • Mongodb logging
  • Verbosity toggle for gff parsing

Changed

  • Meteor version 1.10
  • Node.js version >12
  • MongoDB version 4.2
  • Fully migrated all react components to new hooks API
  • Upgraded to alanning:roles@3.2.0
  • BACKWARDS INCOMPATIBLE: Modified user permission schemas to comply with alanning:roles@3.2.0 for the following collections: users, genomeCollection, genomeSequenceCollection, ExperimentInfo, Transcriptomes. Existing servers attempt to fix this with automatic schema migration.

Fixed

  • Footer correctly displays version info on production builds
  • Plot tooltips can be closed by clicking anywhere on the screen, similar to dropdown menu
  • Various orthogroup loading fixes: results are properly returned to the cli and loading an orthogroup with an existing ID throws an error.

0.1.16 2019-05-02

Added

  • Working 404 page
  • Multiline queries in gene table

Changed

  • Meteor version 1.8.1

Fixed

  • Base url of download links
  • BLAST result options menu
  • Downloads for users that are not logged in
  • Trim whitespace search string
  • Genome selection menu

0.1.15 2019-03-26

Added

  • Download options for annotations and gene expression

Changed

  • Download loading indicators

Fixed

  • Downloading no longer requires user to be logged in

0.1.14 2019-03-21

Added

  • Loading indicator for expression plots
  • View gene expression and protein domains of BLAST hits
  • Link BLAST hits to Gene Table
  • Footer that displays running GeneNoteBook version and links to documentation
  • Warning indicating absence of BLAST databases
  • Set BLAST Parameters
  • Display original input and used parameters of finished BLAST jobs

Changed

  • Orientation of gene expression x-axis to maximize space use

Fixed

  • Expression plots now display scroll on overflow
  • Executables read version info from package.json instead of being hardcoded
  • BLAST databases no longer mysteriously disappear

0.1.13 2018-11-29

Fixed

  • DB path folder creation

0.1.12 2018-11-29

Added

  • --db-path option for genenotebook run to specify location of MongoDB datafiles when letting GeneNoteBook handle the MongoDB daemon.

Changed

  • GeneNoteBook now runs a MongoDB daemon under the hood by default, so having a running MongoDB daemon is no longer a requirement. It is still possible by specifying --mongo-url when executing genenotebook run.
  • Updated to Meteor 1.8.0.1

0.1.11 2018-11-28

Fixed

  • Header logo and font loading when running production bundle on localhost

0.1.10 2018-11-25

Fixed

  • CLI executables logging
  • Header logo
  • Even more font loading fixes
  • Console logging and debugging

0.1.9 2018-11-21

Fixed

  • Font loading for icon fonts
  • Usage string for CLI scripts
  • BLAST url redirect when not logged in

Changed

  • Moved Docker files to separate repository

0.1.8 2018-11-15

Fixed

  • Several GFF3 parsing issues

0.1.7 2018-11-12

Fixed

  • Genetable correctly infers query from URL

Added

  • Spinner indicating that gene table query is loading

Changed

  • Switched to React Router v4
  • Transcriptome sample selection interface

0.1.6 2018-10-30

Fixed

  • Ability to set permission levels of transcriptome samples
  • Gene table column order

Added

  • Genome name column for gene table

0.1.5 2018-10-22

Fixed

  • Correctly set isPublic attribute during genome loading
  • Only admin and curator can edit genes

Changed

  • Updated meteor.js to v1.8.0
  • Cleanup package.json

0.1.4 2018-10-03

Added

  • Ability to change passwords
  • Cancel filter option to GeneTable dropdown menu

Fixed

  • Orthogroup tip labels correctly show on firefox and safari

Changed

  • Color orthogroup tip nodes by organism

0.1.3 2018-09-29

Added

  • Protein domain popovers
  • Gene attributes with multiple values can be toggled to display more or less values
  • Option to download primary transcripts only
  • Add kallisto tsv files from command line

Fixed

  • Parsing newick formatted orthogroup trees and linking genes on gene ID / transcript ID
  • Adding Interproscan gff3 (genenotebook add interproscan)
  • Downloads no longer save empty files

Changed

  • Parsing genome annotation gff3 more efficiently fetches genomic regions and skips (with warning) unrecognized features

0.1.2 2018-08-29

Added

  • Popovers for genemodels

Fixed

  • Searching and dropdown queries no longer conflict

Changed

  • Orthogroup trees are now stored as text and parsed into an object in the browser, since some trees are too big to fit into MongoDB as objects.
  • During the adding of annotations, corresponding sequences are loaded one-by-one in stead of all at once. This fixes memory issues for large genomes.

0.1.1 2018-08-02

Added

  • Executable to add Orthofinder phylogenetic trees (genenotebook add orthogroups)

Fixed

  • Ability to unselect default gene attribute columns in GeneTable view
  • Scanning gene attributes in the admin section now also removes old/unused attributes

0.1.0 - 2018-07-25

Added

  • First GeneNoteBook version ready for use