feat(inventory): support chemical associations for sbmm samples

[adambasha0]

• rather 1-story 1-commit than sub-atomic commits

• commit title is meaningful => git history search

• commit description is helpful => helps the reviewer to understand the changes

• code is up-to-date with the latest developments of the target branch (rebased to it or whatever) => ⏩-merge for linear history is favoured

• added code is linted

• tests are passing (at least locally): we still have some random test failure on CI. thinking of asking spec/examples.txt to be commited

• in case the changes are visible to the end-user,  video or screenshots should be added to the PR => helps with user testing

• testing coverage improvement is improved.

• CHANGELOG :  add a bullet point on top (optional: reference to github issue/PR )

• parallele PR for documentation  on docusaurus  if the feature/fix is tagged for a release

[Copilot]

Pull request overview

This pull request adds support for associating chemical data with sequence-based macromolecule (SBMM) samples, enabling inventory management for proteins and other macromolecules. The feature extends the existing chemical inventory system (previously only available for regular samples) to work with SBMM samples through a new polymorphic association.

Changes:

• Added database migration and foreign key to associate chemicals with SBMM samples
• Implemented exclusive-or validation in Chemical model to ensure it belongs to either a Sample OR an SBMM sample, not both
• Extended frontend ChemicalTab component to support both sample types with conditional rendering (e.g., hiding Safety tab for SBMM)
• Added inventory toggle and tab to SBMM sample details interface

Reviewed changes

Copilot reviewed 20 out of 21 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
db/migrate/20251017_add_sequence_based_macromolecule_sample_id_to_chemicals.rb	Adds foreign key column to link chemicals with SBMM samples
db/migrate/20260220000000_add_inventory_sample_to_sequence_based_macromolecule_samples.rb	Adds inventory_sample boolean flag to SBMM samples
db/migrate/20260220000001_add_index_inventory_sample_to_sequence_based_macromolecule_samples.rb	Adds index on inventory_sample for performance
app/models/chemical.rb	Adds SBMM association with validations ensuring exclusive parent relationship
app/models/sequence_based_macromolecule_sample.rb	Adds has_one :chemical relationship
spec/models/chemical_spec.rb	Tests for parent validation logic (both, neither, one parent scenarios)
spec/factories/chemicals.rb	Factory trait for SBMM-associated chemicals
app/api/chemotion/chemical_api.rb	Updates CRUD endpoints to handle both sample and SBMM types
app/api/helpers/params_helpers.rb	Adds inventory_sample parameter for SBMM samples
app/api/entities/sequence_based_macromolecule_sample_entity.rb	Exposes inventory_sample field
app/javascript/src/components/chemicals/ChemicalTab.js	Adds type parameter, conditional Safety tab, SBMM-specific logic
app/javascript/src/fetchers/ChemicalFetcher.js	Updates fetch/update methods to support both parent types
app/javascript/src/apps/mydb/elements/details/sequenceBasedMacromoleculeSamples/SequenceBasedMacromoleculeSampleDetails.js	Adds inventory checkbox, tab management, and save handlers for chemical data
app/javascript/src/stores/mobx/SequenceBasedMacromoleculeSamplesStore.jsx	Adds chemical edit state management
app/javascript/src/models/SequenceBasedMacromoleculeSample.js	Adds inventory_sample field to model
lib/import/import_collections.rb	Adds sort_data helper to sort imports by creation timestamp
app/javascript/src/apps/mydb/inbox/UnsortedBox.js	Refactors to use bulk delete for better performance
app/javascript/src/stores/alt/actions/InboxActions.js	Fixes array mutation issue in bulk delete
app/javascript/src/stores/alt/stores/InboxStore.js	Handles bulk delete with array of IDs
app/usecases/reactions/update_materials.rb	Comments out equivalent field assignments (likely unrelated change)
app/javascript/src/models/Sample.js	Sets default amount type to 'target' for reference samples
app/javascript/src/apps/mydb/elements/details/VersionsTable.js	Adds message for unsaved elements in history tab
app/javascript/src/apps/mydb/elements/details/VersionsTableChanges.js	Fixes revert button state management
app/javascript/src/apps/mydb/elements/details/VersionsTableFields.js	Adds checkbox change event handler
app/javascript/src/apps/mydb/elements/details/FieldValueSelector.js	Adds null/undefined safety for display value
app/javascript/src/apps/commandAndControl/CnC.js	Improves error handling for device connections
app/api/chemotion/attachment_api.rb	Fixes error response format in bulk delete
config/initializers/novnc_devices.rb	Creates directory for device connection status tracking
app/javascript/src/components/contextActions/import/ModalImport.js	Updates template labels from "Chemical" to "Chemical Sample"
app/javascript/src/apps/mydb/elements/details/reactions/schemeTab/MaterialGroup.js	Adds custom styles to reagent select dropdown
app/javascript/src/apps/mydb/elements/details/sequenceBasedMacromoleculeSamples/propertiesTab/PropertiesForm.js	Simplifies label text

Comments suppressed due to low confidence (1)

app/usecases/reactions/update_materials.rb:281

• The equivalent field is commented out on both update and create operations. If this is intentional and part of this PR's changes, it should be documented why this field is being removed. If this is unintentional or temporary, the commented code should either be removed or restored. This change could potentially break functionality related to reaction equivalents.

        existing_sample.short_label = sample.short_label if sample.short_label
        existing_sample.short_label = fixed_label if fixed_label
        existing_sample.name = sample.name if sample.name
        existing_sample.dry_solvent = sample.dry_solvent
        # Handle components for mixture samples using the proper use case
        if sample.sample_type == Sample::SAMPLE_TYPE_MIXTURE && sample.components.present?
          Usecases::Components::Create.new(existing_sample, sample.components).execute!
        end
        existing_sample.solvent = sample.solvent

        if r = existing_sample.residues[0]
          r.assign_attributes sample.residues_attributes[0]
        end

        existing_sample.container = update_datamodel(sample.container) if sample.container

        existing_sample.skip_reaction_svg_update = true
        existing_sample.save!
        existing_sample

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[Copilot]

ChemicalTab requires a handleUpdateSample prop (marked as required in PropTypes on line 1870), but this prop is not passed when ChemicalTab is used for SBMM samples on line 81-88. This will cause a PropTypes warning and potentially break functionality if handleUpdateSample is called. Either make this prop optional for SBMM usage or provide a handler function.

Suggested change

	editChemical={sbmmStore.editChemical}
	editChemical={sbmmStore.editChemical}
	handleUpdateSample={() => {}}

[Copilot]

The PR title contains a typo: "asssociations" should be "associations" (three 's' instead of two).

[github-actions]

Metrics/ClassLength: Class has too many lines. [205/200]