5.0.3

Version 5.0.3

• DATAUP-641
  • Adds custom error messages when app cell dropdown menu inputs are incorrect in various different ways.
  • Adds custom error messages when app cell checkboxes are initialized with non binary data (should only happen with a bulk import cell from a spreadsheet file)
  • Adds custom error messages when app cell numeric inputs are initialized with non-numeric data.
• PTV-1765 - Fix Pangenome viewer; wasn't able to get an object ref
• DATAUP-643 - Adds a warning to the top of a bulk import cell when attempting to use multiple distinct non-file and non-output parameter values. E.g. different assembly types for multiple rows of an assembly uploader spreadsheet.
• SCT-3162 - Fix download buttons in Data panel widget so that full UPA (with object version) is sent to the downloader app.
• DATAUP-525 - Fix the "show advanced" button in bulk import cells to properly toggle its label when clicked.
• DATAUP-642 - Adds an error message to the bulk import advanced parameters header when closed.
• DATAUP-737 - Overhaul of GitHub Actions to move to using official Docker actions for building, tagging, and uploading images. Move python module installation out of Dockerfile and into the requirements.txt.

Dependency Changes

• Python dependency updates
  • coverage: 5.5 -> 6.2
  • cryptography: 2.7 -> 3.3.2
  • decorator: 5.0.9 -> 5.1.1
  • jinja2: 3.0.1 -> 3.1.1
  • jsonschema: 3.2.0 -> 4.4.0
  • markupsafe: 2.0.1 -> 2.1.1
  • pillow: 8.3.2 -> 8.4.0
  • plotly: 5.3.1 -> 5.6.0
  • pygments: 2.10.0 -> 2.11.2
  • pymongo: 3.12.0 -> 4.1.0
  • pytest-cov: 2.12.1 -> 3.0.0
  • pyyaml: 5.4.1 -> 6.0
  • requests: 2.26.0 -> 2.27.1
  • rsa: 4.7.2 -> 4.8
  • semantic_version: 2.8.5 -> 2.9.0
  • setuptools: 57.4.0 -> 62.0.0
  • sympy: 1.8 -> 1.10.1
  • terminado: 0.11.1 -> 0.13.3

5.0.2

Version 5.0.2

• SAM-73 - Extends the ability to use app params as arguments for dynamic dropdown calls to inputs that are part of a struct or sequence.
• DATAUP-696 - Prevent import specifications from being imported with either unknown data types, or data types not currently registered as using the bulk import cell.
• DATAUP-715 - Adds scrollbars to the configure and results tab of the bulk import cell.
• Fixed an error where Narrative names didn't always render properly in the Narratives panel.
• Fixed an error where Narrative names didn't always render properly in the data slideout.

5.0.1

Version 5.0.1

• SAM-73 - Updated DynamicDropdownInput to have access to full list of other app parameters when user selects dropdown. If an app developer specified to use a certain value from a different field, the field as it currently exists will be used as a parameter.
  Updated AppParamsWidget to return all current values from get-parameters if no specific value was specified, allowing to see all current parameter values without having to know their names.
• DATAUP-570 - Only use the Narrative configuration to set available import types in the Import area dropdowns
• DATAUP-577 - Sanitize suggested output object names for bulk import jobs so they follow the rules
• PTV-1717 - fix landing page links for modeling widgets
• PTV-1726 - address issue where the "Narrative updated in another session" would appear with no other session open

5.0.0

Version 5.0.0

This new major version of the KBase Narrative Interface introduces a way to import data from your data staging area in large batches using a single Bulk Import cell. See more details about the new workflows here: Bulk Import Guide

There are also a ton of other updates and changes to both the Narrative interface (in various small and not-so-small ways) and to how the Narrative software will be developed going forward.

The following is a high level list of changes, with matching JIRA tickets where appropriate. As always, all Narrative work is done on Github and is available for view and discussion there.

Code Changes

• Built an entirely new Bulk Import cell type that runs a batch of Import jobs all at once.
• Objects that can be imported in bulk are:
  • SRA reads
  • Interleaved FASTQ reads
  • Non-interleaved FASTQ reads
  • Read Assemblies
  • GFF metagenomes
  • Genbank genomes
• Redesigned the Data Import Tab
  • It now suggests object upload type based on file suffix.
  • Files are now selected for import by clicking a checkbox (or selecting a type), then clicking “Import Selected”
  • The Import Tab file browser has been improved and remembers selections more consistently
  • The Import Tab styling has been made more internally consistent.
• DATAUP-225 - Styles and color usage have been normalized in many places in the app cell and bulk import cell
• DATAUP-329 - Standardized the use of select boxes in various inputs for the app cell and bulk import cell
• Remove app info dialog option - superseded by the “Info” tab on all app cells
• DATAUP-263 - Fix bug where app cells can get stuck in the “Sending…” phase
• SAM-40 - Add Name/ID column to SampleSet viewer
• DATAUP-651 - Update Data Import tab help tour to include new features.

Development Changes

• UIP-3 - Made the migration away from Bower to using only NPM for Javascript package management. Mostly, the same versions were kept, though some were unavoidably changed
  • seiyria-bootstrap-slider 10.6.2 -> bootstrap-slider 10.6.2 (renamed on npm)
  • plotly.js v1.5.1 -> plotly.js-dist-min v1.50.0 (1.5.1 unavailable)
  • requirejs-plugins 1.0.3 -> 1.0.2 (which is on npm)
  • requirejs-text 2.0.14 -> requirejs/text 2.0.16 (renamed on npm)
  • kbase-ui-plugin-catalog 1.2.14 -> kbase-ui-plugin-catalog 2.2.5 (requires a package.json)
  • Datatables got modified as it was out of date, and there were multiple versions being assembled at once. Now, there's:
    • datatables as a package is obsolete, and supplanted by datatables.net (i.e., we shouldn't have both). Updated from 1.10.9 -> 1.11.3
    • supporting modules (datatables.net-bs, datatables.net-buttons-bs) are the same
      DATAUP-246 - migrate from CSS to using SASS throughout the Narrative, making use of BEM notation for element styling
      DATAUP-62 - designed and implemented simple coding standards and git workflow for the Narrative repo
      DATAUP-71 - added automated linting and code quality tools to the Narrative repo

4.6.0

Narrative version 4.6.0

This introduces the new Narrative Outline view. Click on the "Outline" tab in the left hand panel to see it. It also fixes the Differential Expression Set and Differential Expression Matrix Set viewers, along with a few other maintenance items.

Code changes

• DATAUP-599 - Adjusted the kernel code and tests to account for a Workspace service update.
• PTV-1703 - Fix DifferentialExpressionSet and DifferentialExpressionMatrixSet viewers
• SCT-3088 - Add Narrative Outline View. Allows scrolling through a minimal view of Narrative cells more quickly.

Dependency Changes

• Python dependency updates
  • pillow 8.3.1 -> 8.3.2
  • plotly 5.1.0 -> 5.3.1
  • pygments 2.9.0 -> 2.10.0
  • pytest 6.2.4 -> 6.2.5
  • terminado 0.10.1 -> 0.11.1
• Javascript dependency updates
  • @wdio/browserstack-service 7.9.1 -> 7.11.1
  • @wdio/cli 7.9.1 -> 7.11.1
  • @wdio/local-runner 7.9.1 -> 7.11.1
  • @wdio/mocha-framework 7.9.1 -> 7.11.1
  • @wdio/selenium-standalone-service 7.7.7 -> 7.10.1
  • @wdio/spec-reporter 7.9.0 -> 7.10.1
  • chromedriver 92.0.1 -> 93.0.1
  • husky 7.0.1 -> 7.0.2
  • jasmine-core 3.8.0 -> 3.9.0
  • msw 0.34.0 -> 0.35.0
  • puppeteer 10.1.0 -> 10.4.0
  • terser 5.7.1 -> 5.7.2
  • webdriverio 7.9.1 -> 7.11.1
• Javascript dependency additions
  • expect-webdriverio 3.1.4

4.5.0

• PTV-1561 - SampleSet viewer fixes to allow AMA features; not complete support for AMA features as GenomeSearchUtil does not yet support AMA.
• SCT-3100 - Improve SampleSet viewer; add improved JSON-RPC 1.1 client and associatedKBase service client; add msw (Mock Service Worker) support;
• SCT-3084 - Fixed broken (non-functional) search in the data panel
• SCT-3602 - refseq public data tool now searches by lineage as well; for all public data tools: automatically focus the search input; fix paging bug.
• No ticket - migrate from nosetests to pytest for testing the Python stack.
• Python dependency updates
  • bokeh 2.3.2 -> 2.3.3
  • pillow 8.2.0 -> 8.3.1
  • plotly 4.14.3 -> 5.1.0
  • pymongo 3.11.4 -> 3.12.0
  • pytest 6.2.3. -> 6.2.4
  • pytest-cov 2.11.1 -> 2.12.1
  • requests 2.25.1 -> 2.26.0
  • setuptools 57.0.0 -> 57.4.0
• Javascript dependency updates
  • @types/puppeteer 5.0.0 -> 5.4.4
  • @wdio/browserstack-service 7.7.3 -> 7.9.0
  • @wdio/cli 7.7.3 -> 7.9.0
  • @wdio/local-runner 7.7.3 -> 7.9.0
  • @wdio/mocha-framework 7.7.3 -> 7.9.0
  • @wdio/selenium-standalone-service 7.7.3 -> 7.7.4
  • @wdio/spec-reporter 7.7.7 -> 7.9.0
  • chromedriver 91.0.0 -> 91.0.1
  • eslint 7.28.0 -> 7.32.0
  • husky 6.0.0 -> 7.0.1
  • karma 6.3.3. -> 6.3.4
  • puppeteer 10.0.0 -> 10.1.0
  • selenium-standalone 6.23.0 -> 7.1.0
  • terser 5.7.0 -> 5.7.1
  • wdio-chromedriver-service 7.1.0 -> 7.1.1
  • webdriverio 7.7.3 -> 7.9.1

4.4.0

• boatloads of code cleanup and fixes to the unit and internal testing
• PTV-1635: fix bug in data slideout tab selection
• PTV-1635: fix data and app slideout button and opening behavior
• DEVOPS-475: Change dockerfile so that container runs as nobody, without need to setuid for initialization. Enables removing CAP_SETUID from container initialization
• SCT-2935 - fix refseq public data search behavior to properly restrict the search with multiple terms
• SCT-3038 - refseq public data search now includes genome_id and source_id

4.3.2

• SCT-2778 - convert data slideout, public tab, refseq data source to use searchapi2/rpc api rather than searchapi2/legacy.
• Enhanced integration testing support to add service, host, browser, screen size support.
• Changed the "Dashboard" link in hamburger menu to "Narratives" and use the new /narratives path.

4.3.0

• SCT-2664 - Show the app cell status when in a collapsed state.
• Added an "Info" tab to all app cells with app information.
• Updated links to new KBase home page and docs site.
• Fixed an uploader issue where uploads taking longer than 30 seconds would fail.

4.2.1 Release

• Address problems with SampleSet / AMA Viewer widget.
• SCT-1822 - fix problems with drag and drop data upload failing for more than 100 files (updated the Dropzone widget to version 5.7.0)
• Updated Globus endpoint to point to the newer Globusconnect server.
• Updated tons of dependencies. Thanks Jason Fillman!