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
- Better management for mongo error when adding annotation
- Manage empty genes (no subentities)
- Manage CDS with same IDs in the same gene
- Fix incorrect release
- Hectar loader
- Added /healthcheck endpoint to improve galaxy tool build (Will write a line in logs, and send a 200 response)
- Fixed filtering when using ES search
- Added 'annotation_field" config option, for external ES search
- Added redirection from Gene subentity to Gene in url
- Added 'disable_header' config option, to hide GeneNotebook links and display on the landing page
- Fixed test CI
- Fixed gene list not re-rendering properly when searching
- Fixed search block on the bottom of the landing page
- Error management in expression files
- Option for redirecting the search to an external url ("public.redirectSearch" key in config)
- An additional key "public.redirectSearchAttribute", defaulting to 'query', will be used as the get parameter attribute. (ie: url + "?redirectSearchAttribute=query")
- Options for using a remote search ending, and merging the results with GNB internal search.
- The 'public.externalSearch' option need to be set to true, and an 'externalSearchOptions' dict need to be set.
- 'url' key is the remote endpoint where the query will be sent
- 'gene_field' is the remote field to get the gene IDs (default to geneId)
- 'query_param' : optional get parameter to use for the query
- 'field_param': optional get parameter to use to restrict the results to the gene_field value
- 'count_param': optional get parameter to restrict the number of results
- Multiple annotations for the same genome
- When adding an annotation, you must now set the '--annot' to set the annotation name.
- When integrating data afterward, you can use the --annot tag to specify the annotation you are aiming for.
- If you have multiple genes with the same ID, and do not specify '--annot', the results may be variables
- You can specify --annotations multiple time when integrating orthogroups
- Will now decode proteins and genes IDs when integrating data. (It was already done when integrating gffs, so there was some mismatch with IDs)
- Various UI fixes to better fit multiple annotation versions
- Including an 'annotation' selector in the gene list
- Fix typo in cli
- Fix typo in changelog
- Added generic expression loader
- Crash when loading a transcriptome with a gene not in DB
- Added Hectar loader
- Changed GO API url due to changes
- Break annotation add batch in smaller size units (500 genes)
- Fixed Protein domains view in gene list
- Removed remaining console.log in Eggnog
- Fixed display for blast/diamond when there is no data
- Fixed typo in Show more / Show less for diamond
- Fixed async annotation add
- Added back config file option at startup (see config.json.template)
- Added config option to disable login (and registration) (disable_user_login key)
- Added config option to disable registrations (disable_user_registration key)
- Added config option to hide blast link (disable_blast key)
- Added config option to redirect blast link to custom external link (blast_link key)
- Fixed an issue with annotations files (numerical score values)
- Fixed eggnog integration
- Fixed an issue with publications (stopped loading all interpro / eggnog data)
- Fixed an issue with blast xml loader
- Moved Interpro data to dedicated collection
- Allow multiple blast / interpro results for the same gene (one for each protein)
- Removed wrong link for Unintegrated interpro data
- Disabled Kegg api call (for now)
- Only integrate Interpro & GO DBxref for now
- Fixed several async issues when loading data (interproscan, genome, alignment) (issue with 'on' on LineReader)
- Improper management of errors in CLI (process left hanging)
- Better management of bulkOp when empty
- Add support for custom protein ids when integrating annotation
- Add tests from the API side
- Forked Genenotebook to Genoboo
- Rewrote orthogroup integration (for better protein management + include orthogroup name)
- (Not compatible with previous version: need to re-integrate orthogroups)
- Added Bar Plot for orthogroup content
- API calls for PFAM in Eggnog display (pfam is deprecated)
- Various UI issues
- Support for additional InterproScan file formats (tsv, gff, xml)
- EggNog annotations
- BLAST/diamond alignment reading/visualizing
- User accounts can be added/changed/removed from the CLI
- Bulk operations for user account management through CLI
--dbStartupTimeoutoption togenenotebook runto allow specifying how long to wait for the mongo daemon to start--dbCacheSizeGBoption togenenotebook runto allow specifying how many GBs of RAM can be used for mongodb cache.
- Removed
settings.json - Phylogenetic tree now made with react-bio-viz
- Meteor version 2.5.6
- Once again fixed version display
- Popover menus
- External links and descriptions on GO terms and INTERPRO ids
- Make the list of default user accounts configurable using
settings.jsonconfiguration file - Ability to upload genome sequence through the browser
- Meteor version 2.4
- Node.js version 14
- Option parsing for CLI
- Version display in browser
0.2.0 2020-01-22
- Mongodb logging
- Verbosity toggle for gff parsing
- Meteor version 1.10
- Node.js version >12
- MongoDB version 4.2
- Fully migrated all react components to new hooks API
- Upgraded to
alanning:[email protected] - BACKWARDS INCOMPATIBLE:
Modified user permission schemas to comply with
alanning:[email protected]for the following collections:users,genomeCollection,genomeSequenceCollection,ExperimentInfo,Transcriptomes. Existing servers attempt to fix this with automatic schema migration.
- 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
- Working 404 page
- Multiline queries in gene table
- Meteor version 1.8.1
- 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
- Download options for annotations and gene expression
- Download loading indicators
- Downloading no longer requires user to be logged in
0.1.14 2019-03-21
- 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
- Orientation of gene expression x-axis to maximize space use
- 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
- DB path folder creation
0.1.12 2018-11-29
--db-pathoption forgenenotebook runto specify location of MongoDB datafiles when letting GeneNoteBook handle the MongoDB daemon.
- 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-urlwhen executinggenenotebook run. - Updated to Meteor 1.8.0.1
0.1.11 2018-11-28
- Header logo and font loading when running production bundle on localhost
0.1.10 2018-11-25
- CLI executables logging
- Header logo
- Even more font loading fixes
- Console logging and debugging
0.1.9 2018-11-21
- Font loading for icon fonts
- Usage string for CLI scripts
- BLAST url redirect when not logged in
- Moved Docker files to separate repository
0.1.8 2018-11-15
- Several GFF3 parsing issues
0.1.7 2018-11-12
- Genetable correctly infers query from URL
- Spinner indicating that gene table query is loading
- Switched to React Router v4
- Transcriptome sample selection interface
0.1.6 2018-10-30
- Ability to set permission levels of transcriptome samples
- Gene table column order
- Genome name column for gene table
0.1.5 2018-10-22
- Correctly set isPublic attribute during genome loading
- Only admin and curator can edit genes
- Updated meteor.js to v1.8.0
- Cleanup package.json
0.1.4 2018-10-03
- Ability to change passwords
- Cancel filter option to GeneTable dropdown menu
- Orthogroup tip labels correctly show on firefox and safari
- Color orthogroup tip nodes by organism
0.1.3 2018-09-29
- 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
- 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
- Parsing genome annotation gff3 more efficiently fetches genomic regions and skips (with warning) unrecognized features
0.1.2 2018-08-29
- Popovers for genemodels
- Searching and dropdown queries no longer conflict
- 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
- Executable to add Orthofinder phylogenetic trees (
genenotebook add orthogroups)
- Ability to unselect default gene attribute columns in GeneTable view
- Scanning gene attributes in the admin section now also removes old/unused attributes
- First GeneNoteBook version ready for use