5.4.1

Version 5.4.1

• UIP-51 fix issue where JSON and STAGING download apps aren't getting properly instantiated with object inputs.

Dependency Changes

• Python dependency updates

  • biopython 1.79 -> 1.84
  • bokeh 3.0.3 -> 3.5.1
  • certifi 2024.6.2 -> 2024.7.4
  • chardet 5.0.0 -> 5.2.0
  • ipython 8.25.0 -> 8.26.0
  • networkx 3.0 -> 3.3
  • numpy 1.24.1 -> 2.0.1
  • pexpect 4.8.0 -> 4.9.0
  • pillow 10.3.0 -> 10.4.0
  • plotly 5.13.0 -> 5.23.0
  • pyasn1 0.4.8 -> 0.6.0
  • pygments 2.17.2 -> 2.18.0
  • python-daemon 2.3.2 -> 3.0.1
  • python-dateutil 2.8.2 -> 2.9.0.post0
  • scipy 1.10.0 -> 1.14.0
  • seaborn 0.12.0 -> 0.13.2
  • setuptools 69.5.1 -> 71.1.0
  • sympy 1.10.1 -> 1.13.1
  • ruff 0.4.7 -> 0.5.5

• JavaScript dependency updates

  • @wdio/mocha-framework 8.38.2 -> 8.39.0
  • chrome-launcher 1.1.1 -> 1.1.2
  • chromedriver 126.0.0 -> 126.0.4
  • postcss 8.4.38 -> 8.4.39
  • selenium-webdriver 4.21.0 -> 4.22.0

5.4.0

Narrative Version 5.4.0

• UIP-43
  • Change Narrative JSON downloads to use a download-to-staging app.
  • Add an optional "wildcard" field to app cells that can be used to allow any data object as an app input.
  • Add a text-only output field for app cells to optionally use.
• UIP-44 - Convert data object transform-and-download URLs to use the Blobstore endpoint instead of the Data Import Export service
• UIP-45 - Convert the report object viewer to use the Blobstore endpoint instead of the Data Import Export service
• Remove last references to the Data Import Export service so we can lay it to rest in KBase.

5.3.0

Version 5.3.0

• PTV-1845 - kbaseTabs now shows another tab after a closable tab is closed;
  previously it showed an empty space.
• PTV-1909 - Narrative sign out does sign out
• UIP-41 - Update Jupyter Notebook to version 6.5.6
• UIP-41 - Fix Dropzone dependency issues, address problems with unit tests
• UIP-41 - Removed unused Python dependencies

Notebook widget updates

• The clustergrammer widget was updated to clustergrammer2; see the python dependency changes below for version information.

Dependency Changes

• Updated to include all Python dependencies in the image built in this repo, and removed those that are not directly referenced in KBase code.

• Retained scientific computing dependencies that may be useful to the community (SciPy, numpy, pandas, etc.)

• Removed directly required dependencies that are really just used by the Jupyter Notebook.

• Separated requirements into image dependencies (i.e. packages that are generally useful to have on the Narrative Docker image, ported from the narrative-base-image repo), application requirements and dev requirements.

• Generally useful python packages are combined in the src/requirements-general.txt file.

• the requirements in src/requirements.txt are needed for the Narrative to run.

• the requirements in src/requirements-dev.txt are needed for Narrative development and testing.

• flake8, isort, and black have been replaced by the multifunctional formatter and linter Ruff.

• Python dependency updates

  • beautifulsoup4: 4.12.2 -> 4.12.3
  • black: 24.4.2 -> replaced by Ruff
  • certifi: 2022.12.7 -> 2024.6.2
  • coverage: 7.3.1 -> 7.5.3
  • clustergrammer_widget: removed
  • clustergrammer2: 0.18.0 (new)
  • cryptography: 41.0.4 -> 42.0.8
  • flake8: 7.0.0 -> replaced by Ruff
  • idna: 3.4 -> 3.7
  • isort: 5.13.2 -> replaced by Ruff
  • ipython: 8.10.0 -> 8.25.0
  • jinja2: 3.1.2 -> 3.1.4
  • markupsafe: 2.1.3 -> 2.1.4
  • pillow: 9.4.0 -> 10.3.0
  • pygments: 2.16.1 -> 2.17.2
  • pymongo: 4.5.0 -> 4.7.3
  • pyopenssl: 23.2.0 -> 24.0.0
  • pytest: 7.4.0 -> 8.2.2
  • pytest-cov: 4.1.0 -> 5.0.0
  • pytest-recording: 0.13.1 (new)
  • requests-mock: 1.11.0 -> 1.12.1
  • requests: 2.31.0 -> 2.32.3
  • ruff: 0.4.7 (new)
  • scikit-learn: 1.2.1 -> 1.5.0
  • statsmodels: 0.14.2 (new)
  • terminado: 0.17.1 -> 0.18.0
  • tornado: 6.2 -> 6.4.1
  • vcrpy: 5.1.0 -> 6.0.1

• Javascript dependency updates

  • @babel/traverse: 7.22.8 -> 7.23.3
  • @wdio/browserstack-service: 8.12.2 -> 8.29.3
  • @wdio/cli: 8.12.2 -> 8.29.3
  • axios: 1.4.0 -> 1.6.1
  • chromedriver: 114.0.2 -> 123.0.0
  • commander: 10.0.0 -> 11.1.0
  • dropzone: 5.7.0 -> 5.9.3
  • eslint-config-prettier: 8.8.0 -> 9.1.0
  • follow-redirects: 1.15.2 -> 1.15.4
  • handlebars: 4.7.7 -> 4.7.8
  • karma: 6.4.1 -> 6.4.2
  • nunjucks: 2.4.3 -> 3.2.4 in /src/nodejs/NarrativeServer
  • plotly.js-dist-min: 2.18.2 -> 2.28.0
  • postcss: 8.4.27 -> 8.4.33
  • prettier: 3.0.0 -> 3.2.4
  • puppeteer: 20.8.2 -> 21.10.0
  • pure-uuid: 1.6.4 -> 1.8.1
  • selenium-webdriver: 4.10.0 -> 4.17.0
  • word-wrap: 1.2.3 -> 1.2.4
  • ws: 7.2.0 -> 7.4.6 in /src/nodejs/NarrativeServer

5.2.1

Version 5.2.1

• PTV-1900 - a previous bugfix exposed an issue in the SpeciesTreeBuilder apps. This provides a workaround to keep those apps running.

Dependency Changes

• Python dependency updates
  • coverage: 7.2.7 -> 7.3.0
  • cryptography: 41.0.2 -> 41.0.4
  • pygments: 2.15.1 -> 2.16.1
  • pymongo: 4.4.1 -> 4.5.0

5.2.0

Version 5.2.0

A new feature here is that app cells now store object information internally as UPAs, instead of object names. This will lead to more reproducible results, and is on the path to fixing the long-standing copy-of-a-copy problem.

• PTV-1810 - address object name display issues in the View Configure tab of app cells. This now saves all app inputs as UPAs in the cell. It also includes an update to input transforms to properly convert from UPAs <-> names or references as appropriate before starting the app.
• PTV-1875 - fix public data paging issue by removing paging from workspace data sources
• PTV-1877 - fix app descriptions to replace the documentation link for the upload / download guide
• PTV-1878 - fix some failing front end unit tests
• UIP-28 - update Google Analytics tags to GA4 properties
• UIP-36 - add support for anonymous user ids sent to Google Analytics

Dependency Changes

• Javascript dependency updates

  • @wdio/browserstack-service: 8.10.2 -> 8.12.2,
  • @wdio/cli: 8.10.2 -> 8.12.2
  • @wdio/local-runner: 8.10.2 -> 8.12.1,
  • @wdio/mocha-framework: 8.10.2 -> 8.12.1,
  • @wdio/selenium-standalone-service: 8.10.2 -> 8.14.0,
  • @wdio/spec-reporter: 8.10.2 -> 8.12.2,
  • chromedriver: ^112.0.0 -> ^114.0.0
  • commander: 10.0.0 -> 11.0.0
  • cssnano: 6.0.0 -> 6.0.1
  • datatables.net-buttons-bs: 2.2.3 -> 2.4.1
  • dompurify: none -> 2.3.8
  • eslint: 8.34.0 -> 8.46.0
  • grunt-stylelint: ^0.16.0 -> ^0.19.0
  • karma: ^6.3.16 -> 6.4.2
  • karma-jasmine-html-reporter: 2.0.0 -> 2.1.0
  • numeral: 1.5.0 -> 2.0.6
  • postcss: ^8.3.2 -> 8.4.27
  • postcss-discard-comments: ^5.1.2 -> 6.0.0
  • prettier: 2.7.1 -> 3.0.0
  • puppeteer: 19.8.2 -> 20.8.2
  • pure-uuid: 1.6.2 -> 1.6.4
  • sass: 1.60.0 -> 1.63.6
  • selenium-webdriver: 4.8.0 -> 4.10.0
  • stylelint: ^13.13.1 -> 15.10.2
  • stylelint-config-recommended: ^5.0.0 -> ^13.0.0
  • stylelint-config-sass-guidelines: ^8.0.0 -> ^10.0.0
  • stylelint-config-standard: ^22.0.0 -> ^34.0.0
  • webdriverio: 8.10.2 -> 8.12.3

• Python dependency updates

  • beautifulsoup4: 4.12.1 -> 4.12.2
  • black: 23.3.0 -> 23.7.0
  • coverage: 7.2.2 -> 7.2.7
  • cryptography: 40.0.1 -> 41.0.2
  • flake8: 6.0.0 -> 6.1.0
  • isort: none -> 5.18.0
  • markupsafe: 2.1.2 -> 2.1.3
  • pygments: 2.14.0 -> 2.15.1
  • pymongo: 4.3.3 -> 4.4.1
  • pyopenssl: 23.1.1 -> 23.2.0
  • pytest-cov: 4.0.0 -> 4.1.0
  • pytest: 7.2.2 -> 7.4.0
  • pyyaml: 6.0.0 -> 6.0.1
  • requests: 2.28.2 -> 2.31.0
  • requests-mock: none -> 1.11.0

5.1.3

Version 5.1.3

• PTV-1620 - fix problem with Expression Pairwise Correlation creating or displaying large heatmaps and freezing or crashing browser
• PTV-1514 - sanitized HTML being used for app input tooltips

Dependency Changes

• Python dependency updates
  • black >=20.8b1 -> 22.8.0
  • coverage 6.2 -> 6.4.4
  • cryptography 37.0.4 -> 38.0.1
  • flake8 3.8.4 -> 5.0.4
  • jinja2 3.0.3 -> 3.1.2
  • jupyter-console 6.4.3 -> 6.4.4
  • pygments 2.12.0 -> 2.13.0
  • requests 2.27.1 -> 2.28.1
• Javascript dependency updates
  • @wdio/cli 7.19.6 -> 7.25.0
  • @wdio/local-runner 7.19.5 -> 7.25.0
  • @wdio/spec-reporter 7.19.5 -> 7.25.0
  • bootstrap 3.3.7 -> 3.4.1
  • bootstrap-slider 10.6.2 -> 11.0.2
  • chrome-launcher 0.14.2 -> 0.15.1
  • chromedriver ^101.0.0 -> ^105.0.0
  • cssnano 5.1.7 -> 5.1.13
  • jasmine-core 4.1.0 -> 4.3.0
  • jquery-ui 1.13.1 -> 1.13.2
  • karma-jasmine-html-reporter 1.7.0 -> 2.0.0
  • postcss-cli 9.1.0 -> 10.0.0
  • prettier 2.4.1 -> 2.7.1
  • puppeteer 13.7.0 -> 18.0.5
  • require-css 0.1.8 -> 0.1.10
  • sass 1.51.0 -> 1.55.0
  • selenium-standalone 8.1.1 -> 8.2.0
  • selenium-webdriver 4.1.2 -> 4.4.0
  • terser 5.13.1 -> 5.15.0
  • underscore 1.13.3 -> 1.13.6

Removed dependencies
note a number of these were removed from the narrative, but left in the narrative base image. The requirements.txt in this repo is intended for those packages required for the narrative to run. Any other packages, including scientific programming ones, useful for either KBase Apps or other manual use in Narrative code cells are included in the narrative base image (see narrative-base-image for more details). Also note that most of these are duplicated and included in that image - these are still necessary for narrative functionality when installed locally (i.e. not in a Docker image), so they're left in.

• plotly - not necessary for core narrative functionality, moved to narrative base image
• semantic_version -- removed, wasn't used effectively, and removed the need for it
• sklearn - still included, installed manually alongside clustergrammer in the install script, so the requirements.txt was removed
• sympy - not necessary for core narrative functionality, moved to narrative base image

5.1.2

Version 5.1.2

• PTV-1823 - fixed problem where text input fields for apps were displaying incorrect data on reload
• DATAUP-778 - fixed bug where xsvGenerator would not run if the paramDisplay value was not present
• updated data icon coloring scheme
• refactored narrative Docker image management (see new narrative-base-image repo)

5.1.1

Version 5.1.1

• PTV-1798 - fixed issue where invalid component ID was causing data list not to load properly
• DATAUP-762 - fixed bug where previously run cells were showing errors in the View Configure tab
• DATAUP-763 - fixed an issue where data type icons in the bulk import cell during a run would always show an error, saying that the cell is not ready to run, when it is clearly running.

Dependency Changes

• Python dependency updates
  • cryptography: 36.0.2 -> 37.0.4
  • markupsafe: 2.1.1 -> 2.0.1
  • plotly: 5.7.0 -> 5.9.0
  • rsa: 4.8 -> 4.9
  • semantic_version: 2.9.0 -> 2.10.0

5.1.0

Version 5.1.0

• PTV-1783 - fixed issue where the previous object revert option was unavailable
• DATAUP-639 - fix problems with dynamic dropdown app cell input
  • selected value wasn't being displayed properly after a page reload or cell refresh
  • selected value wasn't being displayed in view-only version
  • "Loading..." message wasn't displayed while fetching data from a service.
  • Update the dynamic dropdown to support the exact_match_on field in app specs.
  • Add a copy button to the dynamic dropdown - this will copy the most relevant text from the dropdown to the clipboard.
    • For dropdowns with an exact_match_on field, this will copy the contents of that field (e.g. for those that present taxonomy ids for a species, this copies just the scientific name)
    • For dropdowns that go against the FTP staging area, this copies the file name and path.
    • For other dropdowns, this copies the formatted text
• DATAUP-751 - add link to staging area docs in the upload tour
• DATAUP-753 - alter the error text for Select input boxes in app cells to be a bit more generalized.
• DATAUP-756 - add a copy button for other, non-dynamic dropdowns. This copies the displayed text to the clipboard.

Dependency Changes

• Javascript dependency updates

  • @wdio/browserstack-service: 7.16.16 -> 7.19.7
  • @wdio/cli: 7.16.16 -> 7.19.6
  • @wdio/local-runner: 7.16.6 -> 7.19.3
  • @wdio/mocha-framework: 7.16.15 -> 7.20.0
  • @wdio/selenium-standalone-service: 7.16.16 -> 7.19.1
  • @wdio/spec-reporter: 7.16.14 -> 7.19.1
  • autoprefixer: 10.2.6 -> 10.4.5
  • commander: 9.0.0 -> 9.3.0
  • chromedriver: 100.0.0 -> 101.0.0
  • corejs-typeahead: 1.6.1 -> 1.3.1
  • datatables.net: 1.11.3 -> 1.12.1
  • datatables.net-bs 1.11.5 -> 1.12.1
  • datatables.net-buttons-bs: 1.4.2 -> 2.2.3
  • ejs: 3.1.6 -> 3.1.7
  • eslint: 8.14.0 -> 8.16.0
  • grunt: 1.4.1 -> 1.5.3
  • grunt-contrib-concat: 1.0.1 -> 2.1.0
  • handlebars: 4.0.5 -> 4.7.7
  • jasmine-core: 4.0.0 -> 4.1.0
  • jquery-nearest: 1.3.1 -> 1.4.0
  • jquery-ui: 1.12.1 -> 1.13.1
  • js-yaml: 3.3.1 -> 3.14.1
  • karma-jasmine: 4.0.1 -> 5.0.1
  • karma-jasmine-matchers: 4.0.2 -> 5.0.0
  • postcss-remove-comments: 5.0.1 -> 5.1.2
  • postcss-cli: 8.3.1 -> 9.1.0
  • postcss-scss: 3.0.5 -> 4.0.4
  • pure-uuid: 1.4.2 -> 1.6.2
  • sass: 1.34.1 -> 1.51.0
  • selenium-standalone: 8.0.9 -> 8.0.10
  • selenium-webdriver: 4.1.1 -> 4.1.2
  • spark-md5: 3.0.0 -> 3.0.2
  • underscore: 1.8.3 -> 1.13.3
  • webdriverio: 7.16.16 -> 7.19.7

• Python dependency updates

  • beautifulsoup4: 4.8.1 -> 4.11.1
  • cryptography: 3.3.2 -> 36.0.2
  • html5lib: 1.0.1 -> 1.1
  • idna: 2.8 -> 3.3
  • jinja2: 3.1.1 -> 3.0.3
  • plotly: 5.6.0 -> 5.7.0
  • pygments: 2.11.2 -> 2.12.0
  • jupyter-console: 6.0.0 -> 6.4.3
  • jsonschema: 4.4.0 -> 3.2.0
  • pymongo: 4.1.0 -> 4.1.1
  • pyopenssl: 19.0.0 -> 22.0.0
  • setuptools: 62.0.0 -> 62.1.0

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