Rosalution - 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.

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat 5 months ago

Rosalution - 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.

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat 7 months ago

Rosalution - 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.

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat 7 months ago

Rosalution - 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.

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat 10 months ago

Rosalution - 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.

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat 12 months ago

Rosalution - 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

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat about 1 year ago

Rosalution - 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

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat about 1 year ago

Rosalution - Rosalution 0.8.1

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 annotation rows to render datasets horizontal if the associated class is included in the rendering configuration. Variant annotations rendered vertically and it took too much space.
• Increased VueJS version to 3.5.12 to use TemplateRef as a feature

Bugs

• Fixed developer API endpoint so that existing analyses can queue their annotations to be rendered again if desired.

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat about 1 year ago

Rosalution - Rosalution 0.8.0

0.8.0

Maintainers

@SeriousHorncat @JmScherer @fatimarabab

Features

• Support for attaching documents, URLs, and Images to fields on an Analysis landing page.
• HTTPs by default for deployments
• Versioning for Annotations as dictated by configuration
• Analyses have a version manifest of annotation's dataset, source, and version
• Render's annotations for an analysis according to it's version manifest
• Timestamped discussions for analyses to which allow users to create, update, and remove text-based messages to each other within an analysis.

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat over 1 year ago

Rosalution - Rosalution: Supporting data accessibility, integration, curation, interoperability, and reuse for precision animal modeling

Maintainers

• @SeriousHorncat
• @JmScherer
• @fatimarabab

New Contributors

• @jbarkley256 made their first contribution in https://github.com/uab-cgds-worthey/rosalution/pull/61

What's Changed

• Importing cases for analysis, with support of automated configured annotations of genomic units with support at curating evidence for analysis review.
• Attachment of supporting evidence as files or URLs
• Support for researchers entering case relevant information to be disseminated to research team
• Multi image attachment for curated figures for analyses
• Attachment of visual annotations associated with genomic units
• Viewing annotations for the genomic units in a case for analysis
• CAS user login, enabling organizations to connect to their Center Authentication Service for user credentials
• Filtering available analyses by data presented on analysis cards in the analysis feed
• Workflows to change analyses from being in preparation to ready, active, approved, declined, on-hold
• 3rd party attachments to link Monday.com and Phenotips URL to the specific analysis

Paper Update

• Updated affiliations to include the country for each of them.

Full Changelog: https://github.com/uab-cgds-worthey/rosalution/compare/0.6.0-er...0.6.1

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat over 2 years ago

Rosalution - Rosalution 0.6.0 - Supporting data accessibility, integration, curation, interoperability, and reuse for precision animal modeling

Maintainers

• @SeriousHorncat
• @JmScherer
• @fatimarabab

New Contributors

• @jbarkley256 made their first contribution in https://github.com/uab-cgds-worthey/rosalution/pull/61

What's Changed

• Importing cases for analysis, with support of automated configured annotations of genomic units with support at curating evidence for analysis review.
• Attachment of supporting evidence as files or URLs
• Support for researchers entering case relevant information to be disseminated to research team
• Multi image attachment for curated figures for analyses
• Attachment of visual annotations associated with genomic units
• Viewing annotations for the genomic units in a case for analysis
• CAS user login, enabling organizations to connect to their Center Authentication Service for user credentials
• Filtering available analyses by data presented on analysis cards in the analysis feed
• Workflows to change analyses from being in preparation to ready, active, approved, declined, on-hold
• 3rd party attachments to link Monday.com and Phenotips URL to the specific analysis

Full Changelog: https://github.com/uab-cgds-worthey/rosalution/compare/0.6.0-er...0.6.0

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat over 2 years ago

Rosalution - Rosalution 0.6.0 - Engineering Release

An engineering release of version 0.6.0 of Rosalution.

What's Changed

• Importing cases for Analysis, resulting in the automated annotation genomic units configured
• Attachment of supporting evidence as files from a researcher's local machine or URLs
• Support for researchers entering case relevant information to be disseminated to research team
  • Attaching an image of a pedigree chart for a case
• Attachment of visual annotations associated with genomic units
• Viewing annotations for the genomic units in a case for analysis
• CAS user login, enabling organizations to connect to their Center Authentication Service for user credentials

Contributors

• @SeriousHorncat
• @JmScherer
• @kuthedk
• @fatimarabab

Full Changelog: https://github.com/uab-cgds-worthey/rosalution/commits/0.6.0-er

Scientific Software - Peer-reviewed - JavaScript
Published by SeriousHorncat almost 3 years ago