Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog. For unreleased changes, see changes.

[1.41.0] - 2025-01-16

Changed

Removed

conflicting github-action release call

[1.40.3] - 2025-01-14

Fixed

release.yaml, applying changes from new version of cargo dist

[1.40.2] - 2025-01-13

Fixed

cargo; upgraded to a version which uses github support macOS version by default

[1.40.1] - 2025-01-10

Fixed

incorrectly named function in cerberus plugin config

[1.40.0] - 2025-01-09

Added

Support for new cerberus version which includes an "ignore" field

Fixed

- Fix Docker container build

[1.39.1] - 2024-11-25

Fixed

[1.39.0] - 2024-11-21

Added

[1.38.0] - 2024-11-19

Added

Changed

[1.37.0] - 2024-10-25

Added

Cardea input format for detailed case summaries

[1.36.1] - 2024-10-09

Fixed

Fix previous jira bugfix which did filter but didn't actually apply it
Fix batchIds fetching in pinery plugin

[1.36.0] - 2024-10-02

Added

Support for API Key as an authentication method Use of API Key in plugin-nabu archive function
Archiving Action as part of the Nabu plugin

Fixed

- Update deprecated dependencies for json-dir-list

[1.35.0] - 2024-08-29

Removed

- Remove unused Grafana data source

Fixed

- Made IntersectionJoin match value/list keys instead of just list/list keys. This makes it match the docs.
Improved title matching for jira plugin

[1.34.2] - 2024-07-15

Fixed

Workaround for jira matching 'close enough' tickets

[1.34.1] - 2024-07-08

Fixed

Fix bug that caused logging level to be ignored

[1.34.0] - 2024-07-08

Added

Logging level for Definer log infrastructure (eg Loki plugin)
Add Standard Output Logger as debugging alternative to Loki plugin.
Debug logging for jira issues

Fixed

Fix comments not applying in some jira updates
Fix compatibility with Jira V3 API
Text search includes vidarr id

[1.33.0] - 2024-05-22

Added

Tag jira actions with their associated verb

Fixed

Publish docker images to ghcr instead of docker.io
Switch jira error logging to using loki plugin if available
Fix Jira transitions failing when a resolution is included in the transition

[1.32.8] - 2024-04-26

Fixed

Stop caches from overloading the log

[1.32.7] - 2024-04-24

Fixed

- Fix build issue with json-dir-list on Windows and MacOS

[1.32.6] - 2024-04-23

Fixed

- Remove users crate from dependency list when building json-dir-list on Windows

[1.32.5] - 2024-04-23

Fixed

- Fix authentication using ShAWK client
Additional server logging for jira errors
- Fix build issue with json-dir-list on Windows and MacOS

[1.32.4] - 2024-04-10

Fixed

Add fix for building rust projects in github actions

[1.32.3] - 2024-04-05

Fixed

Fix jira tickets not closing if open was once generated, and vice versa

[1.32.2] - 2024-03-27

Fixed

Fix module exports in guanyin plugin
- Upgrade and fix logging infrastructure for sshj
Explicitly include bouncycastle to clear SSL errors

[1.32.1] - 2024-03-21

Fixed

Fix modular access errors

[1.32.0] - 2024-03-21

Added

- Actions can be sorted in the UI
- Add new function in JIRA plugin for formatting tables
- Add priority tracing information to Vidarr submission action tiles
- Adds tool to do quick extracts of data from the command line as JSON or delimited text.

Changed

- Move to the Java Platform Module System (JPMS, aka Jigsaw)
- Reorganize documentation
- Show the top few commands for each action

[1.31.2] - 2024-03-12

Fixed

- Fix bug causing wrong field names in serialization

[1.31.1] - 2024-03-05

Fixed

Fixes 'Cannot cast Optional to Set' error; reinstates new Grouping logic

[1.31.0] - 2024-03-04

Added

- Add Vidarr retry failed provision-out command

Fixed

Revert broken grouping rewrite until further fixes can be applied.

[1.30.0] - 2024-02-23

Added

- Adds a new orphaned action filter
- Allow actions to know if the olive is live
- Add IS_LIVE submission policy for Vidarr submit action
- Allow HTTP authentication for -remote input format sources
- Add std::json::encode and std::json::decode functions
- Add new type conversion for dictionaries and JSON values in the Java API
- Add new Count operator for lists
- Allow defining input formats using JSON files
- Add OnReject support to Group clauses

Changed

- Merge JIRA open_ticket and resolve_ticket into a single issue action
- Allow optional consumable resources to be omitted in Vidarr submit actions
- Allow Try It for functions on Definitions page to take JSON or Shesmu input
Remove confusing second generic from cache types
- Replace OnlyIf in Group clause with more sophisticated syntax for handling optionals
Add support for Pinery's HISEQ_ONBOARD workflow type

Removed

- Remove unused ActionState.sortPriority

[1.29.0] - 2024-01-11

Changed

Table files such as .lookup and .commalookup support comments with #

[1.28.0] - 2023-10-26

Changed

Nabu plugin now pulls its configuration from a .nabu file
Update nabu input format name to nabu_file_qc and rename fields to use snake case
Rename fields for case_archive input format to use snake case

Fixed

- Fix placement of action title in UI

[1.27.0] - 2023-09-21

Changed

Vidarr syntax for dry-run argument has changed to the following:
```
submission_policy = DRY_RUN,
```
Allow actions to know when they were last generated

Fixed

Compilation error with multiple Join clauses

[1.26.1] - 2023-09-07T16:53+00:00

Fix 'not a function' errors when Vidarr labels are types other than String

[1.26.0] - 2023-08-17T18:40+00:00

Fix GitHub release workflow
Make simulation more clear when undeclared variables are allowed
Update README files with new requirements, clarifications about plugin-gsi-common
Add Nabu case_archive input format
Add manual workaround to make Vidarr 'priority' consumable resource optional

[1.25.0] - 2023-05-16T17:32+00:00

Replace SFTP file information functions with single stat function
Add Cardea (QC Gate ETL) case_summary input format

[1.24.0] - 2023-04-18T18:08+00:00

Fix OpenAPI schema
Fix Basic filter view saying 'Matches' for negated regex matching
Fix GitHub Pages build by replacing grafana-datasource logo.svg with the original file
Redesign input format cache
Export simulation cache staleness count requests
Fix NPE when action is concurrently purged
Improve error reporting in Simulator when populating caches

[1.23.0] - 2023-02-15T19:54+00:00

Add a gauge to monitor the number of items sent to a refiller
Runscanner -> 1.15.1
Add a paste input source to guided meditations to extract matching strings
Add functions for returning list of names of Accredited and Accredited with Clinical Report projects from Pinery plugin
Remove vidarr-workflow-run:<id> tag from action cards

[1.22.0] - 2023-01-04T19:19+00:00

Update Nabu plugin to use version 3 API
Add swizzle operation
Guided meditation fixes
Fix bad bytecode using signatures after Flatten or Require
Adds new remote jsonconfig plugin
Update Docker build to support BuiltKit, typescript 4.3.2 and Java 17.

[1.21.0] - 2022-11-08T13:26+00:00

Upgrade to Java 17
Add back NIASSA algebraic type so olives may filter

[1.20.0] - 2022-10-13T17:52+00:00

Adds metrics for cache refresh start and end times
Makes source vidarr server explicit for cerberus_fp input_file IDs
Changes swagger contact info to new github issue
Fixes incorrect parameter specification for /constant in swagger

Niassa plugin:

Obliterate this plugin and any references to it.

[1.19.3] - 2022-06-22T19:04+00:00

Display cerberus_fp workflow_version even when workflow version contains four parts (3 for the version and one for the Niassa workflow accession)
Vidarr -> 0.8.0
Cerberus -> 0.2.11

[1.19.2] - 2022-05-25T15:33+00:00

Assign migration action error strings to correct errors list

[1.19.1] - 2022-05-24T20:17+00:00

Fix syntax for string formatting in migration action

[1.19.0] - 2022-05-24T14:08+00:00

Add more informative text to 'input files not yet converted' WAITING migration actions
Fix bug where dumpers are not cleaned up
Doc improvement to clarify how ties are handled in Pick Max/Pick Min
Use the aggregate skip status from cerberus to categorize cerberus_fp records
Runscanner -> 1.13.2
Vidarr -> 0.7.0
Cerberus -> 0.2.10

Issues:

Syntax error in MigrationAction

[1.18.5] - 2022-03-21T19:41+00:00

Revert "Track dumper creation so that they can be stopped and finalized." (See: GP-3243)

[1.18.4] - 2022-03-18T18:47+00:00

Fix confusing errors when ? fails for other reasons1~

[1.18.3] - 2022-03-17T17:58+00:00

Changes:

Pick max fileSWID by path for migration
Track dumper creation so that they can be stopped and finalized.
Update demo data to current data formats
Vidarr -> 0.5.0

[1.18.0] - 2022-01-26T19:25+00:00

Don't show "Retry Failed Workflow" button on Succeeded workflow runs
Add resistance to "Delete & Purge"
Runscanner -> 1.13.1
Vidarr -> 0.4.12

[1.17.0] - 2021-12-09T13:39+00:00

Remove JSON Schema support
Allow action commands to remove other actions
Remove command line tools no one uses
Add cerberus_fp_skipped input format
Add pipedev-skipped cache configuration
Don't include records with a null skip value in CFPSkippedValue
Add skip and stale attributes to cerberus_fp_skipped
Vidarr -> 0.4.11
Cerberus -> 0.2.9

[1.16.0] - 2021-11-10T19:08+00:00

Changes:

Detailed counts about accepted and ignored actions when running bulk commands
Allow creating object fields from a gang
Allow wildcard binding in match
Allow Match to operate on optional types
Add Tabulate syntax for Vidarr retry support
Fix action parameter sorting
Vidarr -> 0.4.10
Cerberus -> 0.2.8

[1.15.4] - 2021-10-15T17:31+00:00

Changes:

Pass timeout variable directly to task runtine block

[1.15.3] - 2021-10-14T17:43+00:00

Changes:

Fix NullPointerException when Vidarr enginePhase is null
Add counter for ssh connection pool errors
Fix instrumental_model in cerberus_fp non-Niassa sample records
Add support for configuring Guanyin report Cromwell task timeout
vidarr -> 0.4.8
cerberus -> 0.2.7

[1.15.2] - 2021-09-15T20:03+00:00

Changes:

Fix case where FAILED Vidarr actions would remain QUEUED indefinitely
Fix typo in Vidarr actions
cerberus -> 0.2.6
vidarr -> 0.4.7

[1.15.1] - 2021-08-13T20:51+00:00

Changes:

Removed debug lines

[1.15.0] - 2021-08-13T18:43+00:00

Changes:

Add Version keyword to syntax
Fixed cases in the server where HttpExchange was not closed
vidarr -> 0.4.6
cerberus -> 0.2.4
run-scanner -> 1.13.0

Pinery changes:

Add pinery_ius_include_skipped input format

[1.14.0] - 2021-07-12T15:30+00:00

Changes:

Filter out individual run-libraries marked as skipped
Fixed NullPointerException when Niassa fetch fails

[1.13.0] - 2021-06-16T17:22+00:00

Changes:

Use processPriority field on ActionState
Prioritize QUEUED and INFLIGHT actions as they need to move quickly
Change scheduler scoring
Add create time to actions
Add workflow run information function
Modify max-in-flight to remove stamp coupling
Sort unfiltered definitions and pause dashboard
Show alerts as "Live" in simulator
Expand documentation for implementation
Upgrade Prometheus Java client
Upgrade Cerberus and Vidarr
Handle null engine parameters for Vidarr actions in UI
Ensure every JSON generator is connected to an object mapper
Fix Vidarr IDs in cerberus_fp
Fix migration action logic
Fix alert query marshalling
Fix switching search on olives page
Fix bug in converting action queries to ECMAScript
Fixes in FAQ

[1.12.2] - 2021-06-03T18:04+00:00

Changes:

Revert change to action scheduler throughput
Fix automatic MIME types in guided meditations (bad JavaScript generated)
Sort elements on definitions page

Vidarr changes:

Handle results from dry-run actions correctly
Fix Vidarr error message for "missing" state. The message displayed was incorrect for the error returned by Vidarr.
Handle null engine phase in Vidarr action

[1.12.1] - 2021-05-31T19:48+00:00

Changes:

Upgrade Cerberus to include new Vidarr version

[1.12.0] - 2021-05-31T14:54+00:00

Changes:

Attempt to mirror HTTP repositories in GitHub action, fixes security failure
Add batches variable to pinery_ius and cerberus_fp
Fix yaml formatting in maven-publish github workflow
Automatically register workflows during migration
Allow polling Vidarr during migration action
Vidarr -> 0.4.2
Updates to operations guide for Vidarr
Add function to extract external ID from external key
fix typo in Vidarr action names
Improve type error messages for algebraic data types

[1.11.0] - 2021-05-19T18:16+00:00

Changes:

Action view UI: include base filter when freezing action view
Guided Meditation UI: add some information about what data was fetched
cerberus -> 0.2.0
Guided meditations actually retry compilation every 2 minutes after failure
Add SAFETY_LIMIT_REACHED to Operations Guide

Language changes:

Add a new Stats collector that produces summary statistics of average, sum, count, minimum, and maximum for numbers in a For expression

Equivalent Strings plugin:

Add a plugin to assess strings which should be treated as equivalent

[1.10.2] - 2021-05-10T20:26+00:00

Changes:

Change this factor which is effectively number of new actions per thread per minute to compensate for the fact that the number of threads has been decreased.
The code generation for Flatten in For did not generate valid ES6

Languages changes:

Create a powerset grouper
Adds a string repeat operation using *, similar to Python
Allow + to work for strings and a type that is convertible to string

Vidarr plugin:

Force HTTP/1.1 version for Vidarr requests

Niassa plugin:

Fix migration action

[1.10.1] - 2021-04-28T18:51+00:00

Changes:

Bug fix in meditation compiler
Redesign thread pools
Create a threading console
MigrationAction to migrate Niassa workflow runs to Vidarr
Show max-in-flight from Vidarr

[1.10.0] - 2021-04-21T17:35+00:00

Changes:

Exception handling for non-main threads
Guided meditations retry compilation every 2 minutes after failure
pipedev -> 2.5.19
Bootstrap Icons -> 1.4.1
'Freeze View' button on Actions and Olives for locking search results
Remove dependency on Apache commons-lang
Remove barberpole animation
Suppress empty JSON file errors
Use new chemistry from Pinery 'flowcell_geometry' variable
Vidarr workflow run actions state tag

[1.9.1] - 2021-04-13T18:37+00:00

Changes:

Force HTTP/1.1 in Guanyin requests
Allow guided meditation to access olives
Allow setting a custom set of clinical projects in Pinery
Use new Java 14 APIs in generated olive code
Relocate bootstrap methods to RuntimeSupport
Allow using custom lookup environment for input formats
Replace PineryClient with new HTTP client
Allow strings to be orderable
Force HTTP/1.1 when fetching input data
Make sure all POST requests have Content-Type
Runscanner 1.12.5
Make First and Reduce order-sensitive and optionals sorted
Create a Tuple collector
Include chromosome lengths in interval plugin
Add a greedy bin splitting function
Fix bug in streaming JSON lists
Add a tool to include genome chromosome information
Expose subproject in pinery_ius and cerberus_fp
Force array length to be integral
Correctly update alert endsAt property

[1.8.8] - 2021-03-31T18:38+00:00

Changes:

Make new Niassa parameter optional
Correct interval plugin JAR name

[1.8.7] - 2021-03-31T17:28+00:00

Changes:

Create a new plugin to handle interval files
Fix compiler bug where Dict would throw ClassCastException
Fix compiler bug where For would fail to compile if a variable name was reused

UI changes:

Fix inability to change some Boolean UI element's state
Make tabs scrollable

Guided meditation changes:

Allow a multiple-fetch operation (For)
Insert the keyword With before Label in form creation syntax
Remove the Flow By keywords
Insert Print before plain text that goes on screen
Rename Fork to For
Change the Repeat and Table constructs to be more like normal For expression with a different keyword (DisplayFor)
Add statuses to end of guided meditations
Create a Let operation in guided meditations
Fix order checking in fetch olive compilation
Fix bugs in Match construct where values in algebraic type were not available as variables
Fix a bug in If where the false branch was not compiled correctly
Allow variables to also be copied into Fetch Olive automatically
Correctly output ECMAScript for For...In... expressions
Ensure empty strings get converted to valid ECMAScript
Fix bug generating ECMAScript for Default and coalesce
Make sure standard functions are available in guided meditations
Correctly distinguish between single strings and string sets parsing action queries
Fix generated action filter for tags in guided meditations

Niassa plugin:

Add a never_ever_launch to Niassa workflow action

Pinery plugin:

Make sure Pinery projects are sorted sets

RunScanner plugin:

Switch to RunScanner incremental fetch interface

SFTP plugin:

Fix SSH connection pooling bug resulting in deadlock/hang

Vidarr plugin:

Create action to unload data from Vidarr
Enable bulk for Vidarr commands
Allow deleting while WAITING_FOR_RESOURCES
Allow reattempting workflow runs in engine phase WAITING_FOR_RESOURCES

[1.8.6] - 2021-03-02T22:07+00:00

Cerberus plugin:

Update version to match Vidarr plugin and deal with schema changes

[1.8.5] - 2021-03-02T14:00+00:00

Changes:

Fix bug where external timestamp checks would result in NPE
Prevent plugin exceptions from breaking the Actions page
Update Docker build to use JDK16 (JDK14+ is required for Vidarr plugin)
Fix compiler error causing exception with generating algebraic object literal

UI changes:

Make number of blocks log-scaled in ordering puzzle just like sequence puzzle
Fix recursive diff operation in UI to handle nulls correctly, return differences found between objects

Guided Meditations changes:

Fetch for constants and functions
Create a fork meditation step to allow "parallel" journeys

Vidarr plugin changes:

Exclude attempt from action equality (resulted in duplicate actions) and include staleness in ID (resulted in missing actions)
Show engine phase per operation
Allow reattemping unstarted workflow runs
Upgrade Vidarr library
Correct Vidarr action tile rendering
Add java.time support to Vidarr JSON object mapper
Allow setting metadata parameters globally for Vidarr

[1.8.4] - 2021-02-23T16:06+00:00

Update to latest Cerberus
Fix incorrect JSON serialisation of algebraic data types
Fix Vidarr submit and status URL
Fix Vidarr INTERNAL type
Fix defining actions for Vidarr workflows

[1.8.3] - 2021-02-22T20:46+00:00

Fix annotations for external_key on pinery_ius and cerberus_fp

[1.8.2] - 2021-02-22T20:21+00:00

Vidarr plugin changes:

Fix vidarr::sign method

[1.8.1] - 2021-02-22T20:04+00:00

Fix release problems

[1.8.0] - 2021-02-22T16:57+00:00

Changes:

Add new Cerberus plugin
Add new Vidarr plugin
Fix import rules for constants and signatures where import did not work
Allow action commands to decide if action state should reset to UNKNOWN

Guided meditations changes:

Create file upload for guided meditations
Fix JavaScript code for literal list
Dump JavaScript guided meditation on failure
Add a dynamic drop down selector to guided meditations
Wrap main guided meditation in Start and ;
Change Fetch and Form syntax to be clearer
Consume leading whitespace in Define meditation parameters
Fix incorrect JavaScript generation in Define meditations
Fix bad JavaScript generation in Flow By Match
Update Fetch Olive syntax
1. It eliminates a bug where callable olives aren't available.
2. It removes the Let syntax and copies all the local variables in the meditation into the simulation.
3. It add the keyword Input before the format name.

JIRA plugin changes:

Only update JIRA ticket labels if available on the JIRA "screen"

[1.7.2] - 2021-02-11T18:35+00:00

Changes:

Read stale data instead of throwing ConcurrentModificationException in cache limiter
Fix bad bytecode when using input variables in Default

UI changes:

Redesign the permutation puzzle

Niassa plugin changes:

Remove concurrency restratint on Niassa and just let Niassa be overloaded

[1.7.1] - 2021-02-08T18:48+00:00

Changes:

Split Niassa and Pinery plugins apart
Allow space in action filter intervals (e.g. last 20 days.

UI changes:

Improve clarity of switch query dialog when the query will be lost

Niassa plugin changes:

Add a concurrency limiter to analysis provenance

[1.7.0] - 2021-02-03T14:42+00:00

Changes:

Fix text query in action search to allow partial matches
Add guided meditations dashboard
Add custom grouper for set combinations
Create a Grafana plugin to access Shesmu action counts

UI changes:

Show complete source path in olive dashboard

Pinery plugin changes:

Clear barcode errors during grouping
Substitute missing sequencer run directories for /

[1.6.5] - 2021-01-21T11:53+00:00

Niassa plugin changes:

Fix exception while getting max-in-flight information

[1.6.4] - 2021-01-20T16:52+00:00

UI changes:

Fix bug preventing Pause Script button from showing

Niassa plugin changes:

Fix extremely slow fetch of max-in-flight information
Include workflow names in max-in-flight Prometheus metrics

[1.6.3] - 2021-01-18T21:04+00:00

Language changes:

Remove date formatter

UI changes:

Change the stats budget to 5 seconds and don't count filtering the actions in that budget.

Niassa plugin changes:

Fix another LIMS key locking prevents locks from being released

[1.6.2] - 2021-01-15T20:13+00:00

Changes:

Track olive execution CPU time
Allow simulating existing olives
Track CPU and wall clock time for cache refreshes

Language changes:

Add new date functions to std::date::
Create object assignment shorthand

UI changes:

Allow saving action IDs from the UI
Allow action and refillers to display things to the user
Show fewer stats based if slow to compute
Fix parsing of some algebraic type descriptors

Niassa plugin changes:

Deal with Niassa's IUS attributes being a incorrect with multiple IUSes
Monitor Niassa cache refresh better
Sign IUS in cerberus_fp and pinery_ius formats

Pinery plugin changes:

Replace Pinery project clinical flag with pipeline

[1.6.1] - 2021-01-07T14:18+00:00

Changes:

Reduce olive thread pool size to avoid overwhelming the machine when running
Fix SSH connection pool and set a maximum connection limit

commit 9c2fccdf80cca35ae27165c80d015e5a726d0ed3 Author: Andre Masella andre.masella@oicr.on.ca Date: Tue Jan 5 17:54:24 2021 -0500

[maven-release-plugin] prepare for next development iteration

[1.6.0] - 2021-01-05T22:45+00:00

Changes:

Provide an endpoint to count the number of matching actions
Add a drain endpoint (purge and download)
Prevent paused scripts from running (in addition to stopping their actions)
Add a new action state for safety interlocks
Export current and max in flight jobs
Allow injection constants during simulation
Add fake refillers to simulator

Language changes:

Allow dumpers to have column names
Allow setting a Label on clauses (to appear in the dataflow diagram)
Fix Dump in join operations to go somewhere

UI changes:

Allow advanced action queries to reference saves searches
Fix bug pretty printing time offsets in advanced action queries
Include generated tags in histograms and stats tables
Allow Drill Down in a new tab
Create a histogram-by-property stats panel
Handle generating a sequence puzzle challenge for 1 action gracefully
Encode URL parameters in a Firefox-friendly way

Niassa+Pinery plugin changes:

Attempt to fix LIMS key locking (again)
Fix Pinery IUS demo data to match the current pinery_ius schema
Copy cerberus_fp gangs to pinery_ius
Fix bug preventing importing .niassawf files in simulation

SFTP/SSH plugin changes:

Add SSH connection pooling

[1.5.0] - 2020-11-18T16:09+00:00

Changes:

Fix incorrect tag regular expression search; regular expression searching on tags was missing results.

Language Changes:

Add IfDefined syntax; This is a new feature meant to operate with coming new features in the simulation dashboard to permit conditional compilation.

UI Changes:

Show the base search on the actions page
Fix sequence generator for dangerous commands to have no duplicates
Fix pager bug where page doesn't advance fully

TSV/Config Changes:

Export bad records from structured config files (.jsonconfig) via Prometheus (shesmu_structured_config_bad_entry)

[1.4.7] - 2020-11-04T19:16+00:00

Language changes:

Add expression to extract capture groups from a regular expression This adds an expression to pull capture groups as a tuple if a regular expression matches. This does them positionally, because Java does not provide an API to get information about named capture groups.
Add functions to create dates from numbers

UI Changes:

Pretty print downloaded JSON files

Pinery Plugin Changes:

Add run_id to pinery_ius

[1.4.6] - 2020-10-30T10:37+00:00

Changes:

Add tag regex action filter to Swagger
Fix regex tag matching in query pretty printer (fixes advanced search)

UI Changes:

Change popup menu calculation again

[1.4.5] - 2020-10-29T11:22+00:00

Changes:

Add a new regular expression filter for action tags
Fix cast class error with join temporary

UI Changes:

Display parse errors for advanced search
Improve advanced search UI feedback This changes the advanced search input box to provide a visual indicator of the query's status and some indication that Enter should be pressed to update.
Fix popup menu positioning again
Fix display of time ranges in basic search
Fix formatting of stats ranges
Fix month selector for time ranges
Refresh searches from server on Actions page The searches provided by the server are populated at page load time. Since searches can be updated based on changes in JIRA, this changes the Actions page to reload the searches every 15 minutes.
Add a button to download SVG diagrams (on both the Olives page and the simulator)
Move counts down in metro diagrams The counts in the metro diagrams are the number of output records and this can be difficult to recognise. This shifts all the counts down by a half row so that the count is between the clause that produced and the clause that consumed it.

Simulator Changes:

Improve extra definitions buttons (make the styling consistent and add a download button)
Improve type parsing and WDL outputs (this allows `wdl_outputs) to be imported correctly)
Allow sharing a script from the simulation console

Niassa Plugin Changes:

Pull more job status information from Cromwell (failure information mostly)

SFTP Plugin Changes:

Improve the SFTP refiller This makes a few improvements to the SFTP refiller:
- perform reading stdout and stderr and writing to stdin in separate threads to avoid buffering
- when reading the first line from the child, it checks that it is OK or UPDATING and complain about it
- kill processes that don't respond appropriately

[1.4.4] - 2020-10-19T10:44+00:00

Changes:

Alerts from Reject or Require clauses now report the line number of the olive rather than the clause.
Data flow counts for Export Define olives are reported better in Prometheus.
Clear counts for .actnow files when deleted

Language changes:

Improve type safety of algebraic types comparisons

UI changes:

Create a new definitions dashboard
Allow ignoring unused variables in simulation
Add groups to Add Filter dialog for actions and alerts
Put buttons and menus of commands in alphabetical order
Improve Export Search dialog
Fixes a bug where deleting entries did not save in Extra Definitions in the simulator and the saved searches on the Actions page.
Fix bug where repeat count was negative (on browser console)
Fix table menu used on the Olives page causing it to look like it should be filtered even though it isn't.
Improve combination locks for dangerous commands
Synchronize settings across tabs
Fix a problem where pop up menus will appear in strange locations on the page.
In advanced search, this attempts to refresh the contents as you type, which overwhelms the backend causing the front end to behave poorly. This waits until enter is pressed.
Add missing icons to Bulk Commands menu

Niassa+Pinery plugin:

Use an algebraic type for pinery::...::platform_for_instrument_model
Fix bug where actions with extra input files were marked as SUCCEEDED instead of HALP.

[1.4.3] - 2020-10-06T10:56+00:00

Changes:

Fix missing signature functions for Export Define
Correctly determine whether output and input formats are the same
Allow Group By discriminators to destructure (e.g., By {run, lane, _} = ius is legal)
Allow Group By discriminators to filter out data using OnlyIf and Univalued
Create a std::string::truncate function
Fix bugs parsing algebraic type signatures
Fix ClassCastExecption bug with Require olives
Fix date formatter

UI changes:

Use Bootstrap icons instead of emoji
Fix Callable Definitions page
Add missing parser in front end for algebraic types
Show number of definitions in Extra Definitions tab in simulator
Create a dashboard for pauses
Make he olive menu is scollable
Make popup menus move with the page content when scolled
Hide UI elements before selections are made
Fix tab switching on data refresh
Add a pane with selected items when doing a multi-select
Make Add Filter → Tags only show relevant tags
Collect action commands in a menu on action tiles
Improve pager layout
Improve navigation and labels in alert display

Niassa+Pinery plugin:

Add workflow kinds to Niassa
Truncate annotations in Niassa to 255 characters
Add new barcode_kit field from v8 Pinery

[1.4.2] - 2020-09-15T18:29+00:00

Changes:

Don't prefix qualified names in join.
Create a new signer accessor when joining against a call (fixes bug using Call)
Fix invalid bytecode generated for Match
Don't require output be used in Export Define olives

UI changes:

Asynchronously fetch tags
Update alert pager UI correctly
Correctly restore state on the Olives page

[1.4.1] - 2020-09-08T19:51+00:00

Changes:

Fix type assignability for tuples and objects

[1.4.0] - 2020-09-08T17:30+00:00

Changes:

Return full-qualified names during binding

UI changes:

Fix error when close callback is called twice
Fix bug where source locations don't get added properly

Language changes:

Add algebraic data types
Allow unused variables if definition is exported

SFTP plugin changes:

Fix json-dir-list thinking some directories were files

Niassa plugin changes:

Fix bug where LIMS key locks are not purged

JIRA plugin changes:

Use complex input field values when transitioning required JIRA fields

[1.3.0] - 2020-09-02T17:52+00:00

Changes:

Create an operations training guide
Don't break status page if loading invalid on-disk input data
Log cache information during exceptions
Make sure all exported definitions are available in simulation
Track the number of unique actions produced for each file
Update demo pinery_ius data to match new format

Language changes:

Add function to get a string's hashcode
Allow exporting and sharing Define olives
Allow getting the action name
Allow joining against Define olive output
Create type accessor for input formats (InputType)
Fix signer accessor hoisting bug

UI changes:

Add search import button
Allow renaming a saved search
Fix flex layout problems in alerts dashboard
Fix start/end times on alerts
Show Export Search button even if there are no actions matched
Streamline UI internals

Config plugin changes:

Add has function for jsonconfig

Niassa plugin changes:

Add override for LIMS key lock
Add additional tests for basesmaks with no indices
Make index 1 handled the same way as index 2 when grouping basemasks

JIRA plugin changes:

Allow default values for required JIRA fields

[1.2.1] - 2020-08-10T18:23+00:00

Niassa/Pinery plugin:

Allow bases masks like y51 to be produced

[1.2.0] - 2020-08-10T15:05+00:00

Changes:

Create a Check pragma
Create intersection join operations
Add min, max and clamp functions
Ignore unknown fields on source locations in REST API
Allow converting advanced searches back into basic
Make exported constants available to script checker

Niassa/Pinery Plugin

Add run_lane_count to pinery_ius
Allow bases masks like y51 to be parsed

Run Scanner plugin:

Expose RunScanner flowcell geometry functions

JIRA plugin:

Add a comment when reopening tickets

SFTP plugin:

Add a fetched date to unix_file
Create a native program to scan directories over SFTP

[1.1.0] - 2020-07-23T17:32+00:00

UI:

Fix bug with advanced search The not-equals/in flag from the queries in the advanced search was being incorrectly disregarded.
Fix event listener on advanced searches
Fix bug where hidden histograms aren't rendered
Fix filter type in crosstab cells
Upgrade to advanced search when basic won't do
Fix popup menu calculations

Niassa/Pinery plugin:

Expose Pinery provider in pinery_project source
Fix HALP state for fixable actions Actions that are fixable (updatable by signatures) should transition to the match's state rather than HALP.
Fix comparison when getting workflow SWID for logging

RunScanner plugin:

Fix incorrect splitting when Run Scanner returns an error The Run Scanner plugin makes the assumption that if it fails to fetch the flowcell geometry, it can return an empty list and downstream processes will consider this an error state. The lane splitting grouper however, did not reject such records. This change rejects them.

[1.0.5] - 2020-07-16T17:03+00:00

Changes:

Fix problem in Actions dashboard causing 400s using server searches
Fix bug causing saved search to default to All Actions on Actions dashboard

[1.0.3] - 2020-07-15T21:19+00:00

Changes:

Remove deployment to non-functional GitHub Packages Maven

[1.0.1] - 2020-07-15T21:06+00:00

Changes:

Fix bug in Docker build process

[1.0.0] - 2020-07-15T20:42+00:00

First official release

Changes:

Fix LIMS key locking issues in Niassa plugin
Create a demo configuration
Add date-from-integer library functions
Fix incorrect start up time on status page
Misc UI fixes and improvements

[0.0.4] - 2020-07-14T18:39+00:00

Changes:

None (developing build process)

[0.0.2] - 2020-07-14T18:36+00:00

Changes:

Start of new release process

Files

RELEASE_NOTES.md

Latest commit

History

RELEASE_NOTES.md

File metadata and controls

Changelog

[1.41.0] - 2025-01-16

Changed

Removed

[1.40.3] - 2025-01-14

Fixed

[1.40.2] - 2025-01-13

Fixed

[1.40.1] - 2025-01-10

Fixed

[1.40.0] - 2025-01-09

Added

Fixed

[1.39.1] - 2024-11-25

Fixed

[1.39.0] - 2024-11-21

Added

[1.38.0] - 2024-11-19

Added

Changed

[1.37.0] - 2024-10-25

Added

[1.36.1] - 2024-10-09

Fixed

[1.36.0] - 2024-10-02

Added

Fixed

[1.35.0] - 2024-08-29

Removed

Fixed

[1.34.2] - 2024-07-15

Fixed

[1.34.1] - 2024-07-08

Fixed

[1.34.0] - 2024-07-08

Added

Fixed

[1.33.0] - 2024-05-22

Added

Fixed

[1.32.8] - 2024-04-26

Fixed

[1.32.7] - 2024-04-24

Fixed

[1.32.6] - 2024-04-23

Fixed

[1.32.5] - 2024-04-23

Fixed

[1.32.4] - 2024-04-10

Fixed

[1.32.3] - 2024-04-05

Fixed

[1.32.2] - 2024-03-27

Fixed

[1.32.1] - 2024-03-21

Fixed

[1.32.0] - 2024-03-21

Added

Changed

[1.31.2] - 2024-03-12

Fixed

[1.31.1] - 2024-03-05

Fixed

[1.31.0] - 2024-03-04

Added

Fixed

[1.30.0] - 2024-02-23

Added

Changed

Removed

[1.29.0] - 2024-01-11

Changed

[1.28.0] - 2023-10-26

Changed