0.8.8-er

Rosalution 0.8.8-er

Maintainers

@SeriousHorncat
@fatimarabab
@JmScherer

Bugs

• Resolved viewport overflow for content within analysis edge cases.

0.8.8

Rosalution 0.8.8

Maintainers

@SeriousHorncat
@fatimarabab
@JmScherer

Features

• The annotations page can select genes & variant of an analysis to view using the page URL's query parameters
• Annotation manifests for analyses are now organized by omic unit, allowing more granular support for versioning of
  annotations.

Bugs

• Opening an analysis' annotation page in a new tab from the analysis page will correctly select the linked gene and
  variant using the query parameters from its URL.
• The annotation page title will no longer include an additional '| ' when there are no variants in the analysis.
• For analyses that include only a gene, the annotation page will no longer attempt to query a non-existent variant from
  the API.

0.8.7

Rosalution 0.8.7

Maintainers

@SeriousHorncat
@JmScherer
@fatimarabab

Features

• Files, links, and existing attachments are attachable to discussion replies within a discussion post thread.
• Content for discussion posts and replies support new lines for multiline content.
• Soft delete support for posts that have threads. A deleted post placeholder rendered when a post with a thread is deleted. The deleted post author, content, and attachments are deleted.
• Rosalution page titles reflect the name of the analysis being viewed. Annotation pages include the analysis' name along with the selected gene and variant.
• The build version of Rosalution is in the footer of each Rosalution page after login.
• Animal model cards are backwards compatible with past and current versions of the JSON schema from Alliance Genome.
• Animal model card titles link out directly to the animal model from their source database if the URL is available.

Bugs

• Missing Favicon with Rosalution's logo on each Rosalution page now present.
• Fixed the styling of Alliance Genome Cards in the Annotation View to display text in a more distinct and readable format.

0.8.6

Rosalution 0.8.6

Maintainers

@SeriousHorncat
@JmScherer
@fatimarabab

Bugs

• Catching HTTP Error exceptions from the Python requests module during annotation; Uncaught HTTPError exceptions cause the annotation background task in FastAPI to crash without completing annotations in the queue.

Rosalution 0.8.5 - Engineering Release

Rosalution 0.8.5 - Engineering Release

Maintainers

@SeriousHorncat
@JmScherer
@fatimarabab

Features

• Discussion Post Threads - Users can collaborate by replying to existing discussion posts in a discussion thread in
  order to capture insights and have relevant conversations with other experts to make more robust decisions on an
  analysis in Rosalution. Also includes support to edit and delete replies a user has authored.
• Caching calls to HTTP datasources configured as a dataset, and forge annotation tasks can be enabled to read value
  from the cached call dataset.
• Caching versions in-memory temporarily when processing annotations. A version is cached used its datasource &
  versioning type.
• Consolidating user experience for Attachments by renaming "Supporting Evidence" to "Attachments" application wide.

Bugs

• Action menu on an analysis' landing page renders as expected when navigating using the 'backwards navigation'
  button in a browser.
• Titles of attachments on discussions now use elipses when the attachment titles are too long to fit on the row.
  Full attachment name is visible by hovering over the attachment with a mouse.

Chores

• Updated Python Backend to not use datetime.utcnow() which is being deprecated.
• Revised invalid HTML DOM that mixed <table> HTML DOM elements within <div>s and <span>s.
• Upgrading jq Python module to 1.8.0 to be to support building the backend for Python 3.13+.
• Consolidated administrative script for adding users to a Rosalution deployment.

0.8.5

Rosalution 0.8.5

Maintainers

@SeriousHorncat
@JmScherer
@fatimarabab

Features

• Discussion Post Threads - Users can collaborate by replying to existing discussion posts in a discussion thread in
  order to capture insights and have relevant conversations with other experts to make more robust decisions on an
  analysis in Rosalution. Also includes support to edit and delete replies a user has authored.
• Caching calls to HTTP datasources configured as a dataset, and forge annotation tasks can be enabled to read value
  from the cached call dataset.
• Caching versions in-memory temporarily when processing annotations. A version is cached used its datasource &
  versioning type.
• Consolidating user experience for Attachments by renaming "Supporting Evidence" to "Attachments" application wide.

Bugs

• Action menu on an analysis' landing page renders as expected when navigating using the 'backwards navigation'
  button in a browser.
• Titles of attachments on discussions now use elipses when the attachment titles are too long to fit on the row.
  Full attachment name is visible by hovering over the attachment with a mouse.

Chores

• Updated Python Backend to not use datetime.utcnow() which is being deprecated.
• Revised invalid HTML DOM that mixed <table> HTML DOM elements within <div>s and <span>s.
• Upgrading jq Python module to 1.8.0 to be to support building the backend for Python 3.13+.
• Consolidated administrative script for adding users to a Rosalution deployment.

0.8.4

Rosalution 0.8.4

Maintainers

@SeriousHorncat
@JmScherer
@fatimarabab

Features

• Discussion Attachments
• Application and VueJS Dataset Component's CSS maintenance and consolidation to resolve rendering layout challenges
  to support upcoming new annotations to visualize.
• Upgraded to FastAPI from 0.110.1 to 0.115.11 to resolve issue that existed until 0.113.0 in FastAPI.
  Optional Multiple File Uploads Broken When Using Pydantic v2.3.0 #10280
• Upgraded python-multipart package in backend dependencies from version 0.0.18 to version 0.0.20 to take
  advantage of FastAPI's type annotations for improved python-multipart.
• New Annotation Task Type, SubprocessAnnotationTask which executes a CLI process to access annotations. Applied
  to running tabix cli tool to fetch DITTO scores from CGDS's public LTS, UAB's long term storage available
  via an S3 interface.

Bugs

• Analyses landing page feed adheres to the CSS grid that structures the application visually. Including the footer,
  and card feed representing each analysis. CSS and HTML DOM streamlined.

0.8.3

Rosalution 0.8.3

Maintainers

@SeriousHorncat
@JmScherer
@fatimarabab

Features

• Rendering layout for annotations of genes and variants are configurable without code update.

0.8.2

Rosalution 0.8.2

Maintainers

@SeriousHorncat
@JmScherer
@fatimarabab

Features

• Added support for attaching genbank (.gb) files for supporting evidence attachments

Development

• Minimum NodeJS version increased to v23.4 to support upgrading package dependencies to avoid reported vulnerabilities
• ESlint upgrade to 9 and migrating configuration to flat file config

Bugs

• Backend starts takes over the shell process allowing it to receive SIGTERM for graceful shutdown

Rosalution 0.8.1

Rosalution 0.8.1

Maintainers

@SeriousHorncat
@JmScherer
@fatimarabab

Features

• Composition API Migration for moving towards real-time collaboration
• New annotation linkouts for COSMIC, and gnomAD4 Variant, and annotations for REVEL and AlphaMissense. New data source
  using OpenCravat. VCF string provided by Ensembl's API is cached in the MongoDB database.
• Updated a row to render datasets horizontal if the associated class is included in the rendering configuration.
  Variant annotations were rendering vertically and it was taking too much space.
• Analyses have a version manifest of annotation's dataset, source, and version
• Increased VueJS version to 3.5.12 to use TemplateRef as a feature
• Added support for attaching genbank (.gb) files for supporting evidence attachments

Development

• Minimum NodeJS version increased to v23.4 to support upgrading package dependencies to avoid reported vulnerabilities
• ESlint upgrade to 9 and migrating configuration to flat file config

Bugs

• Fixed developer API endpoint so that existing analyses can queue their annotations to be rendered again if desired.
• Backend starts takes over the shell process allowing it to receive SIGTERM for graceful shutdown