Extend chemical associations to support sequence based macromolecules samples by adambasha0 · Pull Request #2961 · ComPlat/chemotion_ELN

adambasha0 · 2026-02-17T15:31:25Z

This pull request extends the Chemical model to support associations with sequence-based macromolecules (SBMM) samples in addition to the existing Sample associations. This allows chemicals to be linked to either a Sample or a SequenceBasedMacromolecule sample, enabling better inventory management for both entity types.

Changes:

Added database migration and foreign key to link chemicals to sequence-based macromolecules sample
Implemented mutual exclusivity validations ensuring a chemical belongs to either a sample or SBMM-sample, not both
Extended API endpoints to handle type parameter ('sample' vs 'SBMM') for chemical operations
Updated frontend components to support chemical tab integration in SBMM sample details with conditional rendering

app/models/sequence_based_macromolecule.rb

Copilot

Pull request overview

This pull request extends the Chemical model to support associations with sequence-based macromolecules (SBMM) in addition to the existing Sample associations. This allows chemicals to be linked to either a Sample or a SequenceBasedMacromolecule, enabling better inventory management for both entity types.

Changes:

Added database migration and foreign key to link chemicals to sequence-based macromolecules
Implemented mutual exclusivity validations ensuring a chemical belongs to either a sample or SBMM, not both
Extended API endpoints to handle type parameter ('sample' vs 'SBMM') for chemical operations
Updated frontend components to support chemical tab integration in SBMM sample details with conditional rendering

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
db/migrate/20250902_add_sequence_based_macromolecule_id_to_chemicals.rb	Migration adding sequence_based_macromolecule_id column and foreign key constraint
db/schema.rb	Schema updates reflecting new column and foreign key
app/models/chemical.rb	Added belongs_to association and validations for mutual exclusivity of parent entities
app/models/sequence_based_macromolecule.rb	Added has_one :chemical association
spec/models/chemical_spec.rb	Updated schema annotations (no new tests added)
app/api/chemotion/chemical_api.rb	Extended GET/PUT/POST endpoints to support type parameter and SBMM IDs
app/javascript/src/fetchers/ChemicalFetcher.js	Updated fetch and update methods to handle type-specific parameters
app/javascript/src/components/chemicals/ChemicalTab.js	Added type prop and conditional rendering for safety tab
app/javascript/src/apps/mydb/elements/details/sequenceBasedMacromoleculeSamples/SequenceBasedMacromoleculeSampleDetails.js	Integrated ChemicalTab in SBMM details with inventory tab and save handling
app/javascript/src/apps/mydb/elements/details/samples/SampleDetails.js	Added type="sample" prop to existing ChemicalTab usage
app/javascript/src/stores/mobx/SequenceBasedMacromoleculeSamplesStore.jsx	Added state and actions for chemical save handling in SBMM context

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app/javascript/src/components/chemicals/ChemicalTab.js

app/javascript/src/stores/mobx/SequenceBasedMacromoleculeSamplesStore.jsx

Copilot · 2026-02-17T15:46:54Z

spec/models/chemical_spec.rb

 # frozen_string_literal: true

 # == Schema Information
 #
 # Table name: chemicals
 #
-#  id            :bigint           not null, primary key
-#  cas           :text
-#  chemical_data :jsonb
-#  deleted_at    :datetime
-#  updated_at    :datetime
-#  sample_id     :integer
+#  id                              :bigint           not null, primary key
+#  cas                             :text
+#  chemical_data                   :jsonb
+#  deleted_at                      :datetime
+#  updated_at                      :datetime
+#  sample_id                       :integer
+#  sequence_based_macromolecule_id :bigint
+#
+# Foreign Keys
+#
+#  fk_rails_...  (sequence_based_macromolecule_id => sequence_based_macromolecules.id)
 #


The spec file should include tests for the new validations added to the Chemical model. Specifically, tests should be added to verify that:

A chemical cannot have both sample_id and sequence_based_macromolecule_id set (only_one_parent validation)

A chemical must have at least one of sample_id or sequence_based_macromolecule_id set (at_least_one_parent validation)

A chemical can be successfully created with sequence_based_macromolecule_id instead of sample_id

These are critical business logic validations that should be tested to prevent regressions.

app/models/sequence_based_macromolecule.rb

Copilot · 2026-02-17T15:46:54Z

app/api/chemotion/chemical_api.rb

      params do
-        requires :sample_id, type: Integer, desc: 'sample id'
+        requires :type, type: String, desc: 'chemical type is sample or SBMM'
+        optional :sample_id, type: Integer, desc: 'sample id'
+        optional :sequence_based_macromolecule_id, type: Integer, desc: 'sequence based macromolecule id'
      end


The API endpoints don't validate that the required parent ID is provided based on the type. When type is 'SBMM', sequence_based_macromolecule_id should be required, and when type is 'sample', sample_id should be required. Currently both are optional, which could lead to runtime errors when trying to find_by with a nil ID. Consider adding validation logic to ensure the appropriate ID is present for the given type.

You could omit the type parameter completely and define sample_id and sequence_based_macromolecule_sample_id as mutually exclusive. See https://github.com/ruby-grape/grape?tab=readme-ov-file#mutually_exclusive (exactly_one_of is also a good alternative)

app/api/chemotion/chemical_api.rb

db/migrate/20250902_add_sequence_based_macromolecule_id_to_chemicals.rb

app/javascript/src/components/chemicals/ChemicalTab.js

app/api/chemotion/chemical_api.rb

Copilot

Pull request overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 7 comments.

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app/models/chemical.rb

db/migrate/20260220000002_add_sequence_based_macromolecule_sample_id_to_chemicals.rb

spec/models/chemical_spec.rb

app/javascript/src/fetchers/ChemicalFetcher.js

...lements/details/sequenceBasedMacromoleculeSamples/SequenceBasedMacromoleculeSampleDetails.js

app/javascript/src/components/chemicals/ChemicalTab.js

app/api/chemotion/chemical_api.rb

spec/models/chemical_spec.rb

Copilot

Pull request overview

Copilot reviewed 17 out of 17 changed files in this pull request and generated 4 comments.

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...lements/details/sequenceBasedMacromoleculeSamples/SequenceBasedMacromoleculeSampleDetails.js

app/api/chemotion/chemical_api.rb

db/migrate/20251017_add_sequence_based_macromolecule_sample_id_to_chemicals.rb

app/api/chemotion/chemical_api.rb

spec/api/chemotion/chemical_api_spec.rb

github-actions · 2026-02-26T18:36:37Z

LCOV of commit `fd37662` during CI - Ruby Lint, RSpec, and code coverage #945

Summary coverage rate:
  lines......: 66.9% (18252 of 27299 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

jhmegorei · 2026-02-27T08:33:21Z

app/api/chemotion/chemical_api.rb

      params do
-        requires :sample_id, type: Integer, desc: 'sample id'
+        requires :type, type: String, desc: 'chemical type is sample or SBMM'
+        optional :sample_id, type: Integer, desc: 'sample id'
+        optional :sequence_based_macromolecule_id, type: Integer, desc: 'sequence based macromolecule id'
      end


You could omit the type parameter completely and define sample_id and sequence_based_macromolecule_sample_id as mutually exclusive. See https://github.com/ruby-grape/grape?tab=readme-ov-file#mutually_exclusive (exactly_one_of is also a good alternative)

jhmegorei · 2026-02-27T08:36:09Z

...lements/details/sequenceBasedMacromoleculeSamples/SequenceBasedMacromoleculeSampleDetails.js

  }

+  const updateInventoryTabInCollection = (inventoryOrder) => {
+    if (!currentCollection || currentCollection.is_sync_to_me) return;


Beware, the sync_to_me mechanism is currently being removed/changed. Depending on which PR gets merged first, either you have to update the code referencing collection sharing/synching here or we have to do it in #2783

github-actions · 2026-02-27T08:57:15Z

LCOV of commit `cf09326` during CI - Ruby Lint, RSpec, and code coverage #949

Summary coverage rate:
  lines......: 66.9% (18260 of 27300 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

github-actions · 2026-02-27T11:52:57Z

app/api/chemotion/chemical_api.rb

      params do
        requires :chemical_data, type: Array[Hash], desc: 'chemical data'
        optional :cas, type: String, desc: 'cas number'
+        optional :sample_id, type: Integer


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

…(SBMM) - Add SBMM foreign key to chemicals table and update models for polymorphic-like association - Enforce mutual exclusivity and presence validation for sample_id and sequence_based_macromolecule_id - Update API, fetchers, and UI components to handle both sample- and SBMM-linked chemicals - Extend state management and tests for new association logic - Enable inventory tab functionality for sequence-based macromolecule samples

…les to sequence_based_macromolecule_samples & update chemical api, chemical js fetcher, and migration files

… linkage - return 404 when updating a missing chemical - refresh detail tab ordering when tab props change - persist/hide SBMM inventory tab layout when inventory_sample is toggled - make ChemicalTab sample update callback optional and remove debug logging - consolidate migrations and add indexes for SBMM inventory/chemical relations

github-actions · 2026-02-27T12:07:57Z

LCOV of commit `07d2055` during CI - Ruby Lint, RSpec, and code coverage #960

Summary coverage rate:
  lines......: 66.9% (18259 of 27299 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

github-actions · 2026-02-27T12:11:02Z

LCOV of commit `26fa6f8` during CI - Ruby Lint, RSpec, and code coverage #961

Summary coverage rate:
  lines......: 66.9% (18260 of 27298 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

adambasha0 self-assigned this Feb 17, 2026

Copilot AI review requested due to automatic review settings February 17, 2026 15:31

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Extend chemical associations to support sequence based macromolecules megorei/chemotion_ELN#36

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adambasha0 changed the title ~~Extend chemical associations to support sequence based macromolecules~~ Extend chemical associations to support sequence based macromolecules samples Feb 26, 2026

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adambasha0 added 4 commits February 27, 2026 11:54

refactor

b8f83b4

Refactor: Change chemical association from sequence_based_macromolecu…

6e9828d

…les to sequence_based_macromolecule_samples & update chemical api, chemical js fetcher, and migration files

refactor

daae531

adambasha0 added 7 commits February 27, 2026 11:54

feat: add inventory checkbox to SBMM and refactor

b69fd52

refactor spec tests

2d8c8d9

fix spec tests

be45122

refactor: fix failing spec tests

27192db

refactor: add spec tests for chemical api

8420acd

refactor: use exactly_one_of validator instead of type att

26fa6f8

adambasha0 force-pushed the extend-chemical-associations-to-support-sequence-based-macromolecules branch from 07d2055 to 26fa6f8 Compare February 27, 2026 11:54

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github-actions bot commented Feb 26, 2026

LCOV of commit fd37662 during CI - Ruby Lint, RSpec, and code coverage #945

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LCOV of commit cf09326 during CI - Ruby Lint, RSpec, and code coverage #949

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LCOV of commit 07d2055 during CI - Ruby Lint, RSpec, and code coverage #960

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LCOV of commit 26fa6f8 during CI - Ruby Lint, RSpec, and code coverage #961

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adambasha0 commented Feb 17, 2026 •

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LCOV of commit `fd37662` during CI - Ruby Lint, RSpec, and code coverage #945

LCOV of commit `cf09326` during CI - Ruby Lint, RSpec, and code coverage #949

LCOV of commit `07d2055` during CI - Ruby Lint, RSpec, and code coverage #960

LCOV of commit `26fa6f8` during CI - Ruby Lint, RSpec, and code coverage #961