Aquariumbio Aquarium Versions Save

This version includes the following changes:

• Adds ability for manager to assign jobs to technicians, and improves manager interface for working with jobs. Adds filter for input in job creation interface. A user in technician group now sees dashboard of jobs assigned to them as landing page. Non-admin users no longer see the manager tab.
• Shows natural language dates relative to current time.
• Improve error handling for missing protocol code.
• Improve database connection handling in Krill.
• Improves database organization

Users are encouraged to use the docker image published at hub.docker.com as aquariumbio/aquarium:2.9.0

This version requires database migrations

v2.8.1

This release includes the following changes:

• Krill changes: add technician foot pedal interface (thanks to Abe Miller)
• Add configurable OLA Simple technician page (Abe Miller)
• Change handling of data associations so that only the most recent value of a duplicate key will be displayed. (thanks to Gene Nomicos)
• Change library controller to allow creating library externally with pfish.
• Update entrypoint script to use AWS CloudMap namespace when run on ECS.
• Change object type list to hide internal types.

Contributions from @marikoja , @cashmonger , @Gamemackerel , @gnomicos , and @bjkeller

This release makes Docker configuration the default.

It is no longer necessary for non-developers to clone this repository, and instead users should be using the Docker image available on Docker hub from https://hub.docker.com/r/aquariumbio/aquarium:

• For production deployment, see the deployment instructions at aquarium.bio.
• For a local deployment, clone https://github.com/klavinslab/aquarium-local.

Changes:

• Rewrite entrypoint script so that provides more capabilities for configuring Aquarium.
• Change creation interface for users and groups to make it easier to script adding users.
• Parameterize database and application configuration with environment variables.
• Change puma configuration so that database.yml can contain ERB.
• Flip docker-compose files so that development mode is the default.
• Change Dockerfile to use a multi-stage build with a development stage, a production-build stage, and the stage for the production image.
• Make changes so that asset precompilation can occur in Docker production-build. Includes removing unnecessary monkey patches, and parameterizing database.yml file.
• Consolidated deployment configuration with previous docker configuration, and parameterized configuration using environment variables and a YAML file for instance details. Change S3 configuration to use either S3 or minio based on environment variables.
• Change biofab parameter key to "lab_agreement" and move agreement to YAML file.
• Refactor models to use predicates instead of chained checks of attributes.
• Pull source for aquadoc and anemone into components directory, and add components directory to build.
• Krill changes: add technician foot pedal interface, allow show block note, check, and bullet to take array of strings as arguments.
• Starting Aquarium in production using Docker will print the license.
• Add Sorbet type checking, and simplecov test coverage.

• Changes system menu pages to be more consistent. Changes list pagination to be alphabetical.

• Fixes bug in job execution code that prevented debug operation from manager page.

• Fixes a bug preventing import of collection dimensions.

• Switches Aquarium to MIT License.

• Add rake task to identify protocol dependencies.

• Update sample search to show all items for a sample.

• Update gem and yarn dependencies.

• Fixes bug in recent changes to sample search where results were filtered instead of accumulated and inventory would not be displayed.

• Fixes default date for invoices to use current date.

• Fixes error in json queries where includes were not handled correctly.

• Fixes bug in import where parameters were not being imported properly.

• Fixes error that occurred when browser looked for /favicon.ico

• Makes invoice output easier to read by including names and reordering columns.

• Improves krill error output.

• Update to ruby 2.6.5

• Update gem and yarn dependencies.

Fixes a bug where an empty field type would cause an import to crash.

• Rebuild the invoices page for improved performance that was affecting UW BIOFAB deployment.
• Redesign sample page to simplify interface to move non-sample controls to other pages.
• Refactor protocol and test execution to eliminate redundant code and improve error handling.

Changes Docker configuration so that protocol images can be served by the minio s3 service instead of requiring an external image server.

But, mostly, fixes several issues in Aquarium:

• invoices now scroll and the page no longer crashes when there are no invoices.
• protocol import now properly handles UTF-8 characters, and allows partial types for an operation input/output.
• includes English language tags in HTML page templates so that Chrome doesn't treat Aquarium like it is in Somali.
• jquery is updated to deal with security issue

Fixes a bug in Aquadoc that causes workflow export to fail.

Updates the underlying Rails version to 4.2.11.1 which addresses security issues. If you are upgrading from version 2.4 or earlier, you will need to follow the migration instructions for version 2.5

Also, now imports and exports operation type tests as part of the new publish capability.