version 2 features (#49)

* allow user to direct import to chemotion (#29)

* Chem scanner zip processing (#34)

* Feat/excel import collection (#36)

* Feat/generate molfile ketcher (#40)

* Chore/minor fixes (#43)

* removed rxno from template list
* added documentaiton link, fixed context menu hiding behind inspector
* show kekulized structure of molecule
* fix: restore context menu functionality broken by molecule tooltip, samle delete, hide tooltip on context menu open
* fix: improve SMILES validation to support valid chemical structures, hide keys
* fix: improve Chemotion ELN import compatibility
Add vessel_size, gaseous, log_data to reaction template/schema

* Feat/quill editor (#41)

* Add Quill editor support for analysis content field
  - Update zodSchemes to handle content as both string and object
    - Add transform to automatically parse JSON stringified Delta objects
    - Support Quill Delta format with catchall for additional properties
  - Add content field to analysis extended metadata fields in utils
  - Implement ReactQuill editor for content field rendering
    - Create renderContentField to handle Delta object parsing
    - Support JSON string parsing for imported content
    - Graceful fallback for plain text or empty content
  - Make content field visible in analysis containers

---------

Co-authored-by: Ali Zaib <45627267+alizaib1217@users.noreply.github.com>

Author: phuang26

.gitignore

@@ -39,3 +39,6 @@ cypress/results/*
 cypress/reports/*
 cypress/screenshots/*
 cypress/videos/*
+
+# demo/test data - ignore only specific large test files
+demo-fixtures/export-example.json

cypress/component/chemotion/chemotionApi-simple.cy.ts

@@ -0,0 +1,44 @@
+import { chemotionApi, ChemotionUploadResponse } from '../../../src/services/chemotionApi'
+
+describe('ChemotionApiService - Essential Tests', () => {
+  beforeEach(() => {
+    chemotionApi.clearSession()
+  })
+
+  describe('Session Management', () => {
+    it('should start with no authentication', () => {
+      expect(chemotionApi.isAuthenticated()).to.be.false
+    })
+
+    it('should clear session data', () => {
+      chemotionApi.clearSession()
+      expect(chemotionApi.isAuthenticated()).to.be.false
+    })
+  })
+
+  describe('Upload Without Authentication', () => {
+    it('should fail upload when not authenticated', () => {
+      const blob = new Blob(['test'], { type: 'application/zip' })
+      cy.wrap(chemotionApi.uploadToChemotion(blob, 'test.zip'))
+        .then(result => result as ChemotionUploadResponse)
+        .then((result) => {
+          expect(result.success).to.be.false
+          expect(result.message).to.equal('Not authenticated')
+        })
+    })
+  })
+
+  describe('Error Messages', () => {
+    it('should return proper structure for all responses', () => {
+      const blob = new Blob(['test'], { type: 'application/zip' })
+      cy.wrap(chemotionApi.uploadToChemotion(blob, 'test.zip'))
+        .then(result => result as ChemotionUploadResponse)
+        .then((result) => {
+          expect(result).to.have.property('success')
+          expect(result).to.have.property('message')
+          expect(typeof result.success).to.equal('boolean')
+          expect(typeof result.message).to.equal('string')
+        })
+    })
+  })
+})

cypress/component/helper/excelParser.cy.ts

@@ -0,0 +1,267 @@
+import { parseExcelToExportJson } from '@/helper/excelParser'
+import * as XLSX from 'xlsx'
+
+describe('excelParser', () => {
+  describe('parseExcelToExportJson', () => {
+    it('should parse Excel with samples and reactions', async () => {
+      // Create a simple test Excel file
+      const wb = XLSX.utils.book_new()
+
+      const samplesData = [
+        ['identifier', 'parent', 'name', 'smiles'],
+        ['sample1', 'reaction1', 'Ethanol', 'CCO'],
+      ]
+      const ws_samples = XLSX.utils.aoa_to_sheet(samplesData)
+      XLSX.utils.book_append_sheet(wb, ws_samples, 'Samples')
+
+      const reactionsData = [
+        ['identifier', 'name', 'description'],
+        ['reaction1', 'Test Reaction', 'A test'],
+      ]
+      const ws_reactions = XLSX.utils.aoa_to_sheet(reactionsData)
+      XLSX.utils.book_append_sheet(wb, ws_reactions, 'Reactions')
+
+      // Convert to File
+      const wbout = XLSX.write(wb, { bookType: 'xlsx', type: 'array' })
+      const blob = new Blob([wbout], {
+        type: 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
+      })
+      const file = new File([blob], 'test.xlsx')
+
+      // Parse the file
+      const result = await parseExcelToExportJson(file)
+
+      // Verify structure
+      expect(result).to.have.property('Collection')
+      expect(result).to.have.property('Reaction')
+      expect(result).to.have.property('Sample')
+      expect(result).to.have.property('CollectionsReaction')
+      expect(result).to.have.property('CollectionsSample')
+
+      // Verify we have one collection
+      const collections = Object.values(result.Collection as object)
+      expect(collections).to.have.length(1)
+      expect(collections[0]).to.have.property('label')
+      expect(collections[0].label).to.include('Excel Import')
+
+      // Verify we have one reaction
+      const reactions = Object.values(result.Reaction as object)
+      expect(reactions).to.have.length(1)
+      expect(reactions[0]).to.have.property('name', 'Test Reaction')
+
+      // Verify we have one sample
+      const samples = Object.values(result.Sample as object)
+      expect(samples).to.have.length(1)
+      expect(samples[0]).to.have.property('name', 'Ethanol')
+    })
+
+    it('should parse Excel with only samples', async () => {
+      const wb = XLSX.utils.book_new()
+
+      const samplesData = [
+        ['identifier', 'name', 'smiles'],
+        ['sample1', 'Water', 'O'],
+      ]
+      const ws_samples = XLSX.utils.aoa_to_sheet(samplesData)
+      XLSX.utils.book_append_sheet(wb, ws_samples, 'Samples')
+
+      const reactionsData = [['identifier', 'name']]
+      const ws_reactions = XLSX.utils.aoa_to_sheet(reactionsData)
+      XLSX.utils.book_append_sheet(wb, ws_reactions, 'Reactions')
+
+      const wbout = XLSX.write(wb, { bookType: 'xlsx', type: 'array' })
+      const blob = new Blob([wbout])
+      const file = new File([blob], 'test.xlsx')
+
+      const result = await parseExcelToExportJson(file)
+
+      // Should have collection and sample
+      expect(result).to.have.property('Collection')
+      expect(result).to.have.property('Sample')
+
+      const samples = Object.values(result.Sample as object)
+      expect(samples).to.have.length(1)
+      expect(samples[0]).to.have.property('name', 'Water')
+    })
+
+    it('should handle samples with parent relationships', async () => {
+      const wb = XLSX.utils.book_new()
+
+      const samplesData = [
+        ['identifier', 'parent', 'name'],
+        ['sample1', 'reaction1', 'Parent Sample'],
+        ['sample2', 'sample1', 'Child Sample'],
+      ]
+      const ws_samples = XLSX.utils.aoa_to_sheet(samplesData)
+      XLSX.utils.book_append_sheet(wb, ws_samples, 'Samples')
+
+      const reactionsData = [
+        ['identifier', 'name'],
+        ['reaction1', 'Parent Reaction'],
+      ]
+      const ws_reactions = XLSX.utils.aoa_to_sheet(reactionsData)
+      XLSX.utils.book_append_sheet(wb, ws_reactions, 'Reactions')
+
+      const wbout = XLSX.write(wb, { bookType: 'xlsx', type: 'array' })
+      const blob = new Blob([wbout])
+      const file = new File([blob], 'test.xlsx')
+
+      const result = await parseExcelToExportJson(file)
+
+      // Both samples should be created
+      const samples = Object.values(result.Sample as object)
+      expect(samples).to.have.length(2)
+    })
+
+    it('should handle SMILES in samples', async () => {
+      const wb = XLSX.utils.book_new()
+
+      const samplesData = [
+        ['identifier', 'name', 'smiles'],
+        ['sample1', 'Ethanol', 'CCO'],
+        ['sample2', 'Methanol', 'CO'],
+      ]
+      const ws_samples = XLSX.utils.aoa_to_sheet(samplesData)
+      XLSX.utils.book_append_sheet(wb, ws_samples, 'Samples')
+
+      const reactionsData = [['identifier', 'name']]
+      const ws_reactions = XLSX.utils.aoa_to_sheet(reactionsData)
+      XLSX.utils.book_append_sheet(wb, ws_reactions, 'Reactions')
+
+      const wbout = XLSX.write(wb, { bookType: 'xlsx', type: 'array' })
+      const blob = new Blob([wbout])
+      const file = new File([blob], 'test.xlsx')
+
+      const result = await parseExcelToExportJson(file)
+
+      // Should create molecules for samples with SMILES
+      expect(result).to.have.property('Molecule')
+      const molecules = Object.values(result.Molecule as object)
+      expect(molecules).to.have.length(2)
+    })
+
+    it('should create molecules for all samples (even without SMILES)', async () => {
+      const wb = XLSX.utils.book_new()
+
+      const samplesData = [
+        ['identifier', 'name', 'smiles'],
+        ['sample1', 'Ethanol', 'CCO'],
+        ['sample2', 'No Structure', ''],
+      ]
+      const ws_samples = XLSX.utils.aoa_to_sheet(samplesData)
+      XLSX.utils.book_append_sheet(wb, ws_samples, 'Samples')
+
+      const reactionsData = [['identifier', 'name']]
+      const ws_reactions = XLSX.utils.aoa_to_sheet(reactionsData)
+      XLSX.utils.book_append_sheet(wb, ws_reactions, 'Reactions')
+
+      const wbout = XLSX.write(wb, { bookType: 'xlsx', type: 'array' })
+      const blob = new Blob([wbout])
+      const file = new File([blob], 'test.xlsx')
+
+      const result = await parseExcelToExportJson(file)
+
+      // Should create molecules for ALL samples
+      expect(result).to.have.property('Molecule')
+      const molecules = Object.values(result.Molecule as object)
+      expect(molecules).to.have.length(2)
+
+      // Second sample should have molecule with null SMILES
+      const samples = Object.values(result.Sample as object) as any[]
+      expect(samples).to.have.length(2)
+      samples.forEach((sample) => {
+        expect(sample.molecule_id).to.not.be.null
+        expect(sample.decoupled).to.equal(false)
+      })
+    })
+
+    it('should create reaction-sample links with reactionSchemeType', async () => {
+      const wb = XLSX.utils.book_new()
+
+      const samplesData = [
+        [
+          'identifier',
+          'parent',
+          'name',
+          'reactionSchemeType',
+          'smiles',
+        ],
+        ['sample1', 'reaction1', 'Ethanol', 'startingMaterial', 'CCO'],
+        ['sample2', 'reaction1', 'Acetic Acid', 'reactant', 'CC(=O)O'],
+        ['sample3', 'reaction1', 'Ethyl Acetate', 'product', 'CCOC(C)=O'],
+        ['sample4', 'reaction1', 'Water', 'solvent', 'O'],
+      ]
+      const ws_samples = XLSX.utils.aoa_to_sheet(samplesData)
+      XLSX.utils.book_append_sheet(wb, ws_samples, 'Samples')
+
+      const reactionsData = [
+        ['identifier', 'name', 'description'],
+        ['reaction1', 'Esterification', 'Test reaction'],
+      ]
+      const ws_reactions = XLSX.utils.aoa_to_sheet(reactionsData)
+      XLSX.utils.book_append_sheet(wb, ws_reactions, 'Reactions')
+
+      const wbout = XLSX.write(wb, { bookType: 'xlsx', type: 'array' })
+      const blob = new Blob([wbout])
+      const file = new File([blob], 'test.xlsx')
+
+      const result = await parseExcelToExportJson(file)
+
+      // Verify reaction-sample links were created
+      expect(result).to.have.property('ReactionsStartingMaterialSample')
+      expect(result).to.have.property('ReactionsReactantSample')
+      expect(result).to.have.property('ReactionsProductSample')
+      expect(result).to.have.property('ReactionsSolventSample')
+
+      const startingMaterials = Object.values(
+        result.ReactionsStartingMaterialSample as object,
+      )
+      const reactants = Object.values(result.ReactionsReactantSample as object)
+      const products = Object.values(result.ReactionsProductSample as object)
+      const solvents = Object.values(result.ReactionsSolventSample as object)
+
+      expect(startingMaterials).to.have.length(1)
+      expect(reactants).to.have.length(1)
+      expect(products).to.have.length(1)
+      expect(solvents).to.have.length(1)
+    })
+
+    it('should not create reaction-sample links for samples without reactionSchemeType', async () => {
+      const wb = XLSX.utils.book_new()
+
+      const samplesData = [
+        ['identifier', 'parent', 'name', 'reactionSchemeType', 'smiles'],
+        ['sample1', 'reaction1', 'Ethanol', '', 'CCO'],
+        ['sample2', '', 'Standalone', 'none', 'CO'],
+      ]
+      const ws_samples = XLSX.utils.aoa_to_sheet(samplesData)
+      XLSX.utils.book_append_sheet(wb, ws_samples, 'Samples')
+
+      const reactionsData = [
+        ['identifier', 'name'],
+        ['reaction1', 'Test Reaction'],
+      ]
+      const ws_reactions = XLSX.utils.aoa_to_sheet(reactionsData)
+      XLSX.utils.book_append_sheet(wb, ws_reactions, 'Reactions')
+
+      const wbout = XLSX.write(wb, { bookType: 'xlsx', type: 'array' })
+      const blob = new Blob([wbout])
+      const file = new File([blob], 'test.xlsx')
+
+      const result = await parseExcelToExportJson(file)
+
+      // Should not create any reaction-sample links
+      const startingMaterials = Object.values(
+        result.ReactionsStartingMaterialSample as object,
+      )
+      const reactants = Object.values(result.ReactionsReactantSample as object)
+      const products = Object.values(result.ReactionsProductSample as object)
+      const solvents = Object.values(result.ReactionsSolventSample as object)
+
+      expect(startingMaterials).to.have.length(0)
+      expect(reactants).to.have.length(0)
+      expect(products).to.have.length(0)
+      expect(solvents).to.have.length(0)
+    })
+  })
+})