Refactor eLabFTW conde integration into package

[manulera]

No description provided.

[changeset-bot]

🦋 Changeset detected

Latest commit: 1cb7614

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 8 packages

Name	Type
@opencloning/opencloning-elabftw	Minor
@opencloning/ui	Minor
standalone-app	Patch
syntax-builder	Patch
opencloning	Patch
@opencloning/store	Minor
@opencloning/utils	Minor
test-app	Patch

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[Copilot]

Pull request overview

This PR refactors the eLabFTW database integration into a dedicated workspace package (@opencloning/opencloning-elabftw) and updates the app/UI wiring to consume a database interface via a new DatabaseContext provider. It also standardizes package metadata by adding license: "MIT" and updates test/build tooling to recognize the new package.

Changes:

• Introduces @opencloning/opencloning-elabftw package (interface implementation, shared utilities, Vitest + Cypress tests).
• Adds DatabaseContext to @opencloning/ui and switches apps/opencloning to select/provide the active database interface via context.
• Updates workspace/tooling configs (Vitest workspaces, Cypress/Vite aliases, yarn.lock/resolutions, husky axios check) and adds license fields + changesets.

Reviewed changes

Copilot reviewed 32 out of 45 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
yarn.lock	Adds the new workspace package and wires it into the app dependencies.
vitest.config.js	Includes the new package in Vitest workspace projects.
packages/utils/package.json	Adds MIT license metadata.
packages/ui/src/providers/DatabaseContext.jsx	Adds a DB interface context/provider + hook.
packages/ui/src/hooks/useDatabase.js	Switches useDatabase to come from DatabaseContext.
packages/ui/src/components/dummy/index.js	Exposes dummy DB interface via a stable export path.
packages/ui/package.json	Adds license and exports DatabaseContext + form component entrypoints.
packages/store/package.json	Adds MIT license metadata.
packages/opencloning-elabftw/vitest.config.js	Adds package-local Vitest config and aliases.
packages/opencloning-elabftw/src/utils.js	Shared helpers (error formatting + file fetch).
packages/opencloning-elabftw/src/index.js	Exports eLabFTWInterface from the package.
packages/opencloning-elabftw/src/envValues.js	Reads Vite env configuration for local/dev usage.
packages/opencloning-elabftw/src/eLabFTWInterface.test.js	Adds unit tests for the eLabFTW interface logic.
packages/opencloning-elabftw/src/eLabFTWInterface.js	Implements the eLabFTW OpenCloning DB adapter interface.
packages/opencloning-elabftw/src/common.js	Centralizes axios client + headers + helpers (allowed by husky rule).
packages/opencloning-elabftw/src/SubmitToDatabaseComponent.jsx	Minor cleanup (removes stray whitespace line).
packages/opencloning-elabftw/src/SubmitToDatabaseComponent.cy.jsx	Fixes test imports after package move.
packages/opencloning-elabftw/src/PrimersNotInDatabaseComponent.jsx	Adds UI for saving missing primers during submission.
packages/opencloning-elabftw/src/PrimersNotInDatabaseComponent.cy.jsx	Adds component tests for the new primers UI.
packages/opencloning-elabftw/src/LoadHistoryComponent.jsx	Switches to consuming shared UI RetryAlert.
packages/opencloning-elabftw/src/LoadHistoryComponent.cy.jsx	Adds component tests for loading history.
packages/opencloning-elabftw/src/GetSequenceFileAndDatabaseIdComponent.jsx	Switches to consuming shared UI RetryAlert.
packages/opencloning-elabftw/src/GetSequenceFileAndDatabaseIdComponent.cy.jsx	Fixes test imports after package move.
packages/opencloning-elabftw/src/GetPrimerComponent.jsx	Adds primer selection component.
packages/opencloning-elabftw/src/GetPrimerComponent.cy.jsx	Adds component tests for primer selection behavior.
packages/opencloning-elabftw/src/ELabFTWResourceSelect.jsx	Switches to consuming shared UI PostRequestSelect.
packages/opencloning-elabftw/src/ELabFTWResourceSelect.cy.jsx	Adds component tests for resource search/select.
packages/opencloning-elabftw/src/ELabFTWFileSelect.jsx	Switches to consuming shared UI GetRequestMultiSelect.
packages/opencloning-elabftw/src/ELabFTWFileSelect.cy.jsx	Adds component tests for file selection.
packages/opencloning-elabftw/src/ELabFTWCategorySelect.jsx	Switches to consuming shared UI request wrapper/components.
packages/opencloning-elabftw/src/ELabFTWCategorySelect.cy.jsx	Adds component tests for category selection.
packages/opencloning-elabftw/package.json	Defines the new package (deps/peers/exports).
packages/opencloning-elabftw/README.md	Documents package purpose + env vars + local run instructions.
package.json	Adds license and pins workspace resolution for the new package.
cypress.config.js	Adds alias to the new package for component tests.
apps/test-app/package.json	Adds MIT license metadata.
apps/syntax-builder/package.json	Adds MIT license metadata.
apps/standalone-app/package.json	Adds MIT license metadata.
apps/opencloning/vite.config.js	Adds config option + alias for the new package.
apps/opencloning/src/App.jsx	Selects DB interface (eLabFTW/dummy) and provides via DatabaseProvider.
apps/opencloning/package.json	Adds dependency on @opencloning/opencloning-elabftw + license.
.husky/no_axios_outside_clients.sh	Allows axios usage in new package client module.
.changeset/sweet-tires-deny.md	Changeset for adding license to packages.
.changeset/plain-frogs-dream.md	Changeset for moving eLabFTW integration into its own package.
.changeset/config.json	Links the new package into changeset grouping.

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[codecov]

Codecov Report

❌ Patch coverage is 92.30769% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 86.68%. Comparing base (e2275ad) to head (1cb7614).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
apps/opencloning/src/App.jsx	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #668      +/-   ##
==========================================
+ Coverage   86.66%   86.68%   +0.02%     
==========================================
  Files         229      229              
  Lines        7131     7136       +5     
  Branches     1586     1586              
==========================================
+ Hits         6180     6186       +6     
+ Misses        951      950       -1     

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[manulera]

Hi @NicolasCARPi, I have separated the integration code into a package, that is also published to npm. I think it's good to keep the code separate, and it reinforces the idea that it's truly an integration and not hard-coded into OpenCloning.

Nothing to do on your end, I will test the docker container with eLabFTW and then release again but just wanted to let you know.

The summary of copilot is quite good

[NicolasCARPi]

👍