0.11.3

Switch all visualizers to label.deepcell.org @tddough98 (#201)

This switches all the visualizers to use DeepCell Label with editing enabled.

It also adds visualizer support for the segmentation model. As the segmentation consumer supports different dimension orders, we need to pass this dimension order to DCL to load the images properly. The mesmer redis consumer already sends a dimension order that is forwarded to DCL. I've wired an effect to update the dimension order when the jobForm changes, but this is a bit hacked together and should be revisited as we support flexible dimension orders for more models.

• At the moment, the visualizers are set to label-dev.deepcell.org. Before merging, we should change them to label.deepcell.org after we release 0.4 for deepcell label and put it online.

Merging this will let us take viewer.deepcell.org, spots.deepcell.org, and tracks.deepcell.org offline and close vanvalenlab/deepcell-label#243.

0.11.2

Bump eventsource from 1.1.0 to 1.1.1 @dependabot (#199)

Bumps eventsource from 1.1.0 to 1.1.1.

Changelog

Sourced from eventsource's changelog.

1.1.1

• Do not include authorization and cookie headers on redirect to different origin (#273 Espen Hovlandsdal)

Commits

• aa7a408 1.1.1
• 56d489e chore: rebuild polyfill
• 4a951e5 docs: update history for 1.1.1
• f9f6416 fix: strip sensitive headers on redirect to different origin
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🐛 Bug Fixes

Update name of Polaris example file @elaubsch (#200)

This PR updates the file name for the Polaris example prediction to temporarily address this issue. It also changes the preset suggested channel order for the Polaris job card.

0.11.1

🧰 Maintenance

Add visualizer to jobData for caliban @tddough98 (#197)

This connects the kiosk frontend to the caliban visualizer on tracks.deepcell.org. Now that the field is set for caliban, the View Results button will appear after caliban jobs finish and will submit the result to the visualizer.

0.11.0

🚀 Features

Use different visualizers for each job type @tddough98 (#192)

I reworked how the predict page connects with visualizers so that each prediction pipeline can open results with a different site. The key change are

• remove REACT_APP_LABEL_FRONTEND and LABEL_BACKEND in favor of a visualizer endpoint defined in jobData.js
• update the form sent to the visualizer endpoint
  • The spots visualizer expects this updated form, but I'll need to update the expected form for the mesmer visualizer. This will be a quick pull request into vanvalenlab/deepcell-label#243

As I worked on the Predict component, I separated all the components defined in Predict.js into their own file. Some of the changes beyond copying and pasting into new files are:

• remove unused infoText prop from FileUpload and moved the Grid layout from the Predict component into FileUpload
• remove xs={12} from a Grid in ChannelForm (suggested by a compiler warning)
• rename selectJobType prop in JobForm to jobDropdown to make it clearer that the prop is a React element

There's an addition to .eslintrc.yml to make eslint consistent with prettier autoformatting for switch statements.

🧰 Maintenance

Change default job card settings to match example files @elaubsch (#196)

This PR changes the default settings for the segmentation and Polaris job cards to match the settings needed to analyze the provided example files.

Bump async from 2.6.3 to 2.6.4 @dependabot (#191)

Bumps async from 2.6.3 to 2.6.4.

Changelog

Sourced from async's changelog.

v2.6.4

• Fix potential prototype pollution exploit (#1828)

Commits

• c6bdaca Version 2.6.4
• 8870da9 Update built files
• 4df6754 update changelog
• 8f7f903 Fix prototype pollution vulnerability (#1828)
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This version was pushed to npm by hargasinski, a new releaser for async since your current version.

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Add prettier @tddough98 (#190)

Similar to vanvalenlab/deepcell-datasets#92, I added and ran autoformatting to this repo. Instead of pre-commit, this repo only uses prettier. Pre-commit is better for multi-language projects, but the kiosk-frontend is exclusively a javascript project, so I've opted for a simpler setup. I've followed this guide and added this Prettier GitHub Action as well.

0.10.1

🧰 Maintenance

Update Caliban job card and remove rescale option @msschwartz21 (#188)

• Text on the caliban card is updated and refined
• Resolution scale is removed from the caliban form because it is not enabled in the caliban consumer
• View results option is disabled for caliban

0.10.0

🚀 Features

Add job forms for Segmentation and Caliban consumers @elaubsch (#186)

This PR adds segmentation and Caliban job forms. Because the requirements of each form are all different, they are added as individual files.

Segmentation Form
The job form for the segmentation consumer allows the user to input single channel images of nuclear or whole-cell label channels or a two channel image of nuclear and whole-cell label channels. The channels variable will be used by the segmentation consumer to bring up the nuclear and/or whole-cell models as determined by the channels entered in the form.

Caliban Form
The job form for the Caliban consumer does not have a channels form, because it expects single channel images.

Add more options for Polaris jobs @tddough98 (#182)

This PR introduces two new components MesmerForm and PolarisForm that contain workflow specific forms so that those jobs can be parameterized. The behavior for mesmer is unchanged, which polaris can now pick what segmentation model to use and which channels to use segmentation.

Each Form component updates the jobForm object in the Predict component. We now send the jobForm object to the /predict route, which unpacks the form to send to the consumer. As we expand the supported workflows and the contents of the jobForm varies more, we'll need to revisit how the route handles the jobForm contents.

I've also refactored the ChannelForm to simplify the state for selected channels. Previously, there were four collaborating variables that tracked the selected channels including:

• targetChannels like { nuclei: 'red', cytoplasm: 'green' }
• channels like ['red, 'green', 'blue']
• channelValues like { red: 0, green: 1, blue: 2}
• requiredChannels like ['nuclei', 'cytoplasm']

These variables had to be transformed between each other with complex expression like
Object.keys(channels).reduce((r, c) => Object.assign(r, { [channels[c]]: parseInt((r[channels[c]] || '').concat(c)) }), {}) and requiredChannels.map(c => channelValues[targetChannels[c]]).

I've refactored these variables into just requiredChannels ['nuclei', 'cytoplasm'] and selectedChannels [0, 1] which records which channel index should be used for each required channel. The selectedChannels are more similar to the data submitted to the api and is transformed with a simple expression selectedChannels.join(',') to yield 0,1. I've also moved ['red', 'green', 'blue'] to an internal detail of the ChannelDropdown component as it is only used in display text.

🧰 Maintenance

Bump minimist from 1.2.5 to 1.2.6 @dependabot (#187)

Bumps minimist from 1.2.5 to 1.2.6.

Commits

• 7efb22a 1.2.6
• ef88b93 security notice for additional prototype pollution issue
• c2b9819 isConstructorOrProto adapted from PR
• bc8ecee test from prototype pollution PR
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Bump url-parse from 1.5.7 to 1.5.10 @dependabot (#185)

Bumps url-parse from 1.5.7 to 1.5.10.

Commits

• 8cd4c6c 1.5.10
• ce7a01f [fix] Improve handling of empty port
• 0071490 [doc] Update JSDoc comment
• a7044e3 [minor] Use more descriptive variable name
• d547792 [security] Add credits for CVE-2022-0691
• ad23357 1.5.9
• 0e3fb54 [fix] Strip all control characters from the beginning of the URL
• 61864a8 [security] Add credits for CVE-2022-0686
• bb0104d 1.5.8
• d5c6479 [fix] Handle the case where the port is specified but empty
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0.9.0

🚀 Features

Polaris consumer @elaubsch (#179)

Adding Polaris to predictions types

• Added Polaris to job cards
• Removing "View Results" button from Polaris job card until coordinate spot location labels are compatible with DeepCell Label

🧰 Maintenance

Bump nanoid from 3.1.20 to 3.2.0 @dependabot (#180)

Bumps nanoid from 3.1.20 to 3.2.0.

Changelog

Sourced from nanoid's changelog.

Change Log

This project adheres to Semantic Versioning.

3.2

• Added --size and --alphabet arguments to binary (by Vitaly Baev).

3.1.32

• Reduced async exports size (by Artyom Arutyunyan).
• Moved from Jest to uvu (by Vitaly Baev).

3.1.31

• Fixed collision vulnerability on object in size (by Artyom Arutyunyan).

3.1.30

• Reduced size for project with brotli compression (by Anton Khlynovskiy).

3.1.29

• Reduced npm package size.

3.1.28

• Reduced npm package size.

3.1.27

• Cleaned dependencies from development tools.

3.1.26

• Improved performance (by Eitan Har-Shoshanim).
• Reduced npm package size.

3.1.25

• Fixed browserify support.

3.1.24

• Fixed browserify support (by Artur Paikin).

3.1.23

• Fixed esbuild support.

3.1.22

• Added default and browser.default to package.exports.

3.1.21

• Reduced npm package size.

Commits

• 23b1369 Release 3.2 version
• 967788e Remove TS test tools
• 27eaa90 Simplify new binary tool
• a9d9123 Update dependencies
• 32b9bda Allows passing size or custom alphabet via cli as args (#334)
• 246d5f8 Update vite
• afdf9c9 doc: Fixed Typo (#335)
• 90a446f Update benchmark results
• 8ba2319 bench: add @​napi-rs/uuid v4 (#333)
• f425778 Release 3.1.32 version
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Bump follow-redirects from 1.14.4 to 1.14.7 @dependabot (#177)

Bumps follow-redirects from 1.14.4 to 1.14.7.

Commits

• 2ede36d Release version 1.14.7 of the npm package.
• 8b347cb Drop Cookie header across domains.
• 6f5029a Release version 1.14.6 of the npm package.
• af706be Ignore null headers.
• d01ab7a Release version 1.14.5 of the npm package.
• 40052ea Make compatible with Node 17.
• 86f7572 Fix: clear internal timer on request abort to avoid leakage
• 2e1eaf0 Keep Authorization header on subdomain redirects.
• 2ad9e82 Carry over Host header on relative redirects (#172)
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0.8.2

🐛 Bug Fixes

Rename tracking to caliban. @willgraf (#176)

0.8.1

Bump axios from 0.21.1 to 0.21.2 @dependabot (#174)

Bumps axios from 0.21.1 to 0.21.2.

Release notes

Sourced from axios's releases.

v0.21.2

0.21.2 (September 4, 2021)

Fixes and Functionality:

• Updating axios requests to be delayed by pre-emptive promise creation (#2702)
• Adding "synchronous" and "runWhen" options to interceptors api (#2702)
• Updating of transformResponse (#3377)
• Adding ability to omit User-Agent header (#3703)
• Adding multiple JSON improvements (#3688, #3763)
• Fixing quadratic runtime and extra memory usage when setting a maxContentLength (#3738)
• Adding parseInt to config.timeout (#3781)
• Adding custom return type support to interceptor (#3783)
• Adding security fix for ReDoS vulnerability (#3980)

Internal and Tests:

• Updating build dev dependancies (#3401)
• Fixing builds running on Travis CI (#3538)
• Updating follow rediect version (#3694, #3771)
• Updating karma sauce launcher to fix failing sauce tests (#3712, #3717)
• Updating content-type header for application/json to not contain charset field, according do RFC 8259 (#2154)
• Fixing tests by bumping karma-sauce-launcher version (#3813)
• Changing testing process from Travis CI to GitHub Actions (#3938)

Documentation:

• Updating documentation around the use of AUTH_TOKEN with multiple domain endpoints (#3539)
• Remove duplication of item in changelog (#3523)
• Fixing gramatical errors (#2642)
• Fixing spelling error (#3567)
• Moving gitpod metion (#2637)
• Adding new axios documentation website link (#3681, #3707)
• Updating documentation around dispatching requests (#3772)
• Adding documentation for the type guard isAxiosError (#3767)
• Adding explanation of cancel token (#3803)
• Updating CI status badge (#3953)
• Fixing errors with JSON documentation (#3936)
• Fixing README typo under Request Config (#3825)
• Adding axios-multi-api to the ecosystem file (#3817)
• Adding SECURITY.md to properly disclose security vulnerabilities (#3981)

Huge thanks to everyone who contributed to this release via code (authors listed below) or via reviews and triaging on GitHub:

• Sasha Korotkov
• Daniel Lopretto
• Mike Bishop
• Dmitriy Mozgovoy
• Mark
• Philipe Gouveia Paixão

... (truncated)

Changelog

Sourced from axios's changelog.

0.21.2 (September 4, 2021)

Fixes and Functionality:

• Updating axios requests to be delayed by pre-emptive promise creation (#2702)
• Adding "synchronous" and "runWhen" options to interceptors api (#2702)
• Updating of transformResponse (#3377)
• Adding ability to omit User-Agent header (#3703)
• Adding multiple JSON improvements (#3688, #3763)
• Fixing quadratic runtime and extra memory usage when setting a maxContentLength (#3738)
• Adding parseInt to config.timeout (#3781)
• Adding custom return type support to interceptor (#3783)
• Adding security fix for ReDoS vulnerability (#3980)

Internal and Tests:

• Updating build dev dependancies (#3401)
• Fixing builds running on Travis CI (#3538)
• Updating follow rediect version (#3694, #3771)
• Updating karma sauce launcher to fix failing sauce tests (#3712, #3717)
• Updating content-type header for application/json to not contain charset field, according do RFC 8259 (#2154)
• Fixing tests by bumping karma-sauce-launcher version (#3813)
• Changing testing process from Travis CI to GitHub Actions (#3938)

Documentation:

• Updating documentation around the use of AUTH_TOKEN with multiple domain endpoints (#3539)
• Remove duplication of item in changelog (#3523)
• Fixing gramatical errors (#2642)
• Fixing spelling error (#3567)
• Moving gitpod metion (#2637)
• Adding new axios documentation website link (#3681, #3707)
• Updating documentation around dispatching requests (#3772)
• Adding documentation for the type guard isAxiosError (#3767)
• Adding explanation of cancel token (#3803)
• Updating CI status badge (#3953<...

0.8.0

🚀 Features

Open predict page results in Label @tddough98 (#159)

Once a job is complete, we add an Open In Label button that sends a form to the Label backend to create a project, and then opens the project in the Label frontend.

The Predict component now

• fetches dimensionOrder from Redis, then forwards the dimensionOrder to Label backend to create a project from the uploaded image
• has been refactored to move some elements into their own components

Also, I changed the default jobtypes to match the current jobtypes so the kiosk frontend works right off the bat when developing from a fresh repo.

Replace `ScaleForm` with new `ResolutionDropdown`. @willgraf (#171)

As discussed in #165, the ScaleForm is a bit too unintuitive for users. It's not clear what the correct "scale" should be. This PR replaces the ScaleForm with a manual dropdown with common microns-per-pixel values (and the zoom level used with them). This way, the user can select if their data is 40x or 10x instead of trying to guess at the correct scale.

I think there is still room for a manual input form for image mpp, but for now, I think that the ballpark resize values will be helpful and intuitive.

Fixes #165

Update Footer to include a link to GitHub. @willgraf (#162)

Refactor About and FAQ pages for better information. @willgraf (#156)

• Replace Data page with a link to datasets.deepcell.org.
• Only show top-level error if NODE_ENV is set to production.
• Fix mobile menu rendering.
• Remove redundant information from FAQ page (lots of info is also on About).
• Update FAQ to remove references to the DeepCell Kiosk and instead route users to intro-to-deepcell.
• Add new Swagger component to fix routing 404 issues.

Fixes #155, Fixes #161

🧰 Maintenance

Bump url-parse from 1.5.1 to 1.5.3 @dependabot (#170)

Bumps url-parse from 1.5.1 to 1.5.3.

Commits

• ad44493 [dist] 1.5.3
• c798461 [fix] Fix host parsing for file URLs (#210)
• 201034b [dist] 1.5.2
• 2d9ac2c [fix] Sanitize only special URLs (#209)
• fb128af [fix] Use 'null' as origin for non special URLs
• fed6d9e [fix] Add a leading slash only if the URL is special
• 94872e7 [fix] Do not incorrectly set the slashes property to true
• 81ab967 [fix] Ignore slashes after the protocol for special URLs
• ee22050 [ci] Use GitHub Actions
• d2979b5 [fix] Special case the file: protocol (#204)
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Bump path-parse from 1.0.6 to 1.0.7 @dependabot (#169)

Bumps path-parse from 1.0.6 to 1.0.7.

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Update dependencies for security. @willgraf (#168)

• Update swagger-ui-react to ^3.51.2
• Update concurrently to ^6.2.0

Bump ssri from...