v2.6.0

This release enhances a feature introduced in the previous version

Minor features:

• The URLs for the services used to obtain external links for genes and regions are no longer assumed to have a particular structure in the config file, but instead information about the gene or region is substituted into a URL template via placeholder representations.

v2.5.0

This release updates dependencies and introduces a new feature.

Minor features:

• External links for a region on a chromosome can now be dynamically loaded from a service specified in the config file. Currently genes and micro-synteny tracks utilize this service via their detail panes.

v2.4.0

This release fixes some bugs, updates dependencies, and introduces a handful of new features.

Major features:

• The format of the text in the macro-synteny legend can now be configured via the top-level macro-synteny legend configuration; this formatted text is what's used when coloring the macro-synteny legend and tracks
• Macro-synteny colors are now automatically assigned if a coloring script is not provided in the configuration

Minor features:

• Macro-synteny colors are now a top-level macro-synteny legend configuration instead of a per-server configuration
• The help widget is now available on all pages, not just in the gene view

Bug fixes:

• The search widget now contains the search present in the URL query string params even when the page is loaded from a URL or via in app navigation

v2.3.0

This release fixes some bugs, updates dependencies, and introduces a handful of new features. Notably, all files related to Docker Compose have been moved to a separate, independently versioned repository: legumeinfo/gcv-docker-compose.

Major features:

• Default parameter values can now be set from the config file (see the Wiki for details)
• Instructions page screenshots now support responsive image sizing and each image has a lightbox for closer inspection (see the Wiki for details)
• A scale-screenshot command has been added to the NPM package CLI to allow admins to generate scaled copies of screenshots to support responsive sizing in production
• "Advanced" chromosome genes and chromosome length parameters have been added to the macro-synteny parameters to allow users to only generate blocks for chromosomes that have a minimum number of genes and/or a minimum physical length (bp), respectively

Minor features:

• The macro-synteny distance metric now uses multiset Jaccard instead of regular Jaccard
• Distance is now the default macro-synteny ordering scheme used when one isn't specified
• The Redis loader is now a service in the microservices Docker Compose files, though it is not automatically run with Docker Compose up
• Multiple alignments no longer contain empty columns
• The micro-synteny gene family legend now emits the names of the genes in a family via the broadcast channel when a family in the legend is hovered over
• The togglable orphans gene family feature from v1 of GCV was reimplemented
• The GCV path (base href) can now be set in Docker via the GCV_PATH environment variable in the production container

Bug fixes:

• Updated the RediSearch heath check to prevent microservices from starting before the database is loaded
• Automatic Redis snapshots are now disabled since our access pattern is write once, read many, which fixes a bulk loading bug
• Added the node_modules/ directory as a volume in the development container
• Changing the micro-synteny search parameters now actually triggers a new search instead of just clearing the view
• Resizing a viewer's container no longer resets the container's scroll position

v2.2.0

This release completes the transition of the backend from a Django project built on Chado (PostgreSQL) to a microservices architecture built on Redis. It also introduces new major/minor features and fixes some bugs.

Major features: Use of microservices (the Django server has been deprecated and the microservices have been moved to another repository), support for gRPC-Web.

Minor Features: Dependency updates, extensive use of Docker Compose.

Per usual, this release also continues to refactor internal code. This does not effect the user and systems operators but will continue to improve performance while facilitating maintainability and extensibility.

Lastly, this release introduces automated builds and publishing of Docker images to GitHub packages, meaning systems operators can now deploy the GCV and its microservices using only pre-built container images.

v2.1.1

This release updates the various project dependencies. No new features are added.

v2.1.0

This release fixes some bugs, updates dependencies, and introduces fuzzy gene and chromosome region searching.

Major features: Fuzzy gene and chromosome region searching via a search widget in the application header and the search URL.

Minor features: Reimplemented loading a new context via dragging and dropping the current region highlight bar in the macro-synteny viewer. The project has now been containerized via Docker Compose.

The backend that supports fuzzy search and chromosome region queries is implemented as containerized microservices that utilize a Redis database. This is the beginning of a transition of the backend from Django and Chado (PostgreSQL) to microservices and Redis. During this transition both the Django and microservices backends must be run in tandem to fully support the frontend client.

v2.0.0

This is the second major release of the Genome Context Viewer.

Major features: A new data model, a new services API, a user configurable UI, the "search" and "multi" views have been merged into a single "genes" view and pairwise dot plots are now only available on-demand, though users can control their placement in the view.

Minor features: Alerts have been replaced with process pipelines, macro tracks can now be ordered and searched, a new micro track clustering algorithm, pervasive use of tooltips for meta data and help text.

This release also includes major revisions to the structure and organization of the client code. Though this has little impact on users, the quality of the code has been greatly improved, making it easier to maintain and extend moving forward.

v1.4.1

This release fixes some minor bugs and updates dependencies. No new features.

v1.4.0

This release fixes some bugs, updates dependencies, and introduces a couple new features.

Minor features: Tooltips, sources description in instructions view, and description of parameters in form widget.

Major features: Span-based searches and inter-application communication.