[Feature] Add editable table with PDF file matching for PDF-only uploads

[Copilot]

Description

This PR adds an editable table interface for PDF-only uploads, allowing users to manually create reference entries and assign PDFs when no bibliography file is provided.

Core Changes:

• Automatic table generation: Shows editable table when PDFs uploaded without bibliography, initializes with 3 empty rows
• Multi-select PDF assignment: Files column uses Tabulator list editor with multiselect, dynamically populated from uploaded PDFs
• Reference validation: Enforces unique + required constraints on reference column, required on files column
• Unmapped PDF tracking: Displays count and list of PDFs not assigned to any reference
• Real-time analysis sync: Edits to reference/files columns trigger analysis status updates via deep watch on dataframe data hash

Implementation:

// Dynamic columns with PDF multi-select
editableTableColumns: [
  { field: "reference", frozen: true, validator: ["required", "unique"] },
  { field: "files", frozenRight: true, editor: "list", 
    editorParams: { values: pdfFileOptions, multiselect: true } }
]

// Auto-sync table edits to dataframe format
handleTableCellEdit(cell) {
  editableTableData = editableTable.getData()
  syncEditableTableToBibData()  // Converts to TableData with filePaths
}

Data Flow:
PDFs uploaded → shouldShowEditableTable → User edits → syncEditableTableToBibData → Analysis pipeline

Leverages existing BaseSimpleTable/RenderTable components and domain entities (TableData, DataFrameSchema). Backward compatible—bibliography upload hides table and resumes standard flow.

Related Tickets & Documents

Closes #191

What type of PR is this? (check all applicable)

• Refactor
• Feature
• Bug Fix
• Optimization
• Documentation Update

Steps to QA

1. Upload PDF files without a bibliography file
2. Verify editable table appears with reference, title, authors, year, journal, doi, files columns
3. Edit reference column → verify unique validation (duplicate values rejected)
4. Click files column → verify multi-select dropdown shows all uploaded PDFs
5. Assign PDFs to references → verify unmapped PDF count updates below table
6. Upload bibliography file afterward → verify table disappears and standard flow resumes
7. Check import analysis → verify status reflects manual entries

Added/updated tests?

• Yes
• 8 unit tests in useImportFileUploadViewModel.spec.ts covering table visibility, column configuration, unmapped tracking, and data sync

Added/updated documentations?

• No, and this is why: MVP feature, documentation can be added in follow-up based on user feedback
• I need help with writing docs

Checklist

• I have added relevant notes to the CHANGELOG.md file (See https://keepachangelog.com/)

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Add Editable Table with File Path Matching for PDF-Only Uploads</issue_title>
<issue_description># Add Editable Table with File Path Matching for PDF-Only Uploads

Problem

When users upload PDFs without bibliography files, they currently have no way to create reference entries or match PDFs to file paths for extraction. This limits the usefulness of the PDF-first upload flow.

Solution

Create a MVP editable table interface that allows users to:

1. Generate reference entries from uploaded PDFs (initially start with an empty editable table)
2. Manually edit reference metadata (title, authors, etc.)
3. Match PDFs to file paths for extraction
4. Add custom reference keys

Requirements

Core Functionality

1. Automatic Table Generation: When PDFs are uploaded without bibliography files, automatically generate an empty table with reference and files columns
2. Editable Fields: Allow editing and adding additionally columns (title, authors, year, journal, DOI, etc.) (already implemented in RenderTable)
3. File Path Matching: Listing uploaded PDFs that have mapped to the metadata table entries or not

UI Components

1. Table Interface: Data table with inline editing capabilities
2. File Matching: multi-selection interface to match 1 or more PDFs to each reference
3. Metadata Extraction: Extract basic metadata from PDF headers/OCR when possible

Integration Points

1. PDF Processing: Extract metadata from uploaded PDFs on the backend
2. File Matching Logic: Intelligent matching based on filename patterns, extracted titles, etc.
3. Fallback Creation: Generate placeholder entries when metadata extraction fails

Files to Modify

• extralit-frontend/components/features/import/file-upload/ImportFileUpload.vue :
  • Integrate new table creation flow with editable table (by default) and validators for unique value in the reference column.
  • Additionally the files column (frozen right) need to be a multi value list editor where user can multi-select the uploaded pdf file paths to each reference, configured in tableColumns passed to BaseSimpleTable. See https://tabulator.info/docs/6.3/edit#editor-list
  • Potentially need to create list of PDF files not yet mapped to a reference
• extralit-frontend/components/features/import/analysis/useImportAnalysisTableViewModel.ts, trigger update on status on cell edits on reference or files column.

Files for reference

• extralit-frontend/v1/domain/services/FileMatchingService.ts - only run when a BIB/CSV file uploaded for the initial pdf file mapping
• extralit-frontend/components/features/import/file-upload/CsvColumnSelection.vue - only use for field mapping (column renaming to reference column) with uploaded CSV

Acceptance Criteria

• Users can upload PDFs and get an editable table of reference entries
• Table allows inline editing of all reference fields
• PDF-to-entry matching works multi-select
• Uses existing validators for files and reference column

Dependencies

• Depends on completion of Issue Reverse File Upload Order: PDF Upload First, Then Table Upload #165 (PDF-first upload order)
• Backend PDF metadata extraction API</issue_description>

Comments on the Issue (you are @copilot in this section)

Custom agent used: ddd-architect
Delivers high-quality, production-ready codebases grounded in domain-driven design principles with clear, pragmatic documentation.

• Fixes Add Editable Table with File Path Matching for PDF-Only Uploads #166

---

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[Copilot]

Pull request overview

This PR adds an editable table interface for PDF-only uploads, enabling users to manually create reference entries and assign PDF files when no bibliography file is provided. The feature automatically displays an editable table with reference metadata columns when PDFs are uploaded without a bibliography file, supports multi-select PDF assignment via Tabulator's list editor, enforces validation constraints, and tracks unmapped PDFs in real-time.

Changes:

• Implements automatic table generation with 3 empty rows when PDFs are uploaded without bibliography
• Adds multi-select PDF file assignment with dynamic dropdown in the "files" column
• Integrates real-time analysis updates through deep watching of dataframe data hash
• Includes comprehensive unit tests covering table visibility, column configuration, and data synchronization

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
useImportFileUploadViewModel.ts	Core view model implementing editable table logic, column configuration with validators, unmapped PDF tracking, data sync, and auto-submit watcher
useImportFileUploadViewModel.spec.ts	Unit tests covering table visibility conditions, column configuration, unmapped file tracking, and data synchronization
ImportFileUpload.vue	Template integration of BaseSimpleTable component with editable table section and unmapped PDFs display
useImportAnalysisTableViewModel.ts	Adds deep watch on dataframe data hash to trigger analysis updates on cell edits
BaseSimpleTable.vue	Handles validators prop and spreads column properties to preserve editor config
RenderTable.vue	Spreads column properties in config and emits cell-edited event

Comments suppressed due to low confidence (1)

extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.ts:448

• The reset function should also clear editableTableData to ensure a clean state when resetting the component. Currently, the editable table data persists after reset, which could lead to stale data being displayed if the user resets and then uploads PDFs again.

  const reset = () => {
    // Set flag to prevent recursive updates during reset
    isInitializing.value = true;
    hasAutoSubmitted.value = false;
    // Reset bibliography data
    bibData.value = {
      fileName: "",
      dataframeData: null,
      rawContent: "",
    };


    // Reset PDF data
    pdfData.value = {
      matchedFiles: [],
      unmatchedFiles: [],
      totalFiles: 0,
    };

[Copilot]

There's no test coverage for the auto-submit behavior when all PDFs are mapped. Consider adding a test that verifies the watcher triggers syncEditableTableToBibData when unmappedPdfFiles becomes empty and sets hasAutoSubmitted to prevent duplicate submissions.

[Copilot]

There's no test coverage for the handleTableCellEdit and handleTableBuilt event handlers. Consider adding tests to verify that these handlers properly sync the table data with editableTableData.

[Copilot]

There's no test coverage for the initializeEditableTable function. Consider adding a test to verify that it creates 3 empty rows with the correct structure when PDFs are uploaded without bibliography.

[priyankeshh]

Suggested change

	if (
	editableTable.value &&
	newUnmapped.length === 0 &&
	!hasAutoSubmitted.value
	) {
	if (
	editableTable.value &&
	editableTableData.value.length > 0 &&
	newUnmapped.length === 0 &&
	!hasAutoSubmitted.value
	) {

We’re currently checking only editableTable.value to determine readiness, but the table instance may exist before it has actual row data.

Consider also checking editableTableData.value.length > 0 to ensure the table is fully initialized before triggering auto-submit. This prevents premature submission when PDFs are first uploaded.

[priyankeshh]

Suggested change

	const handleTableCellEdit = (cell: any) => {
	const handleTableCellEdit = (_cell: any) => {

[priyankeshh]

Suggested change

	const initialRows = Array.from({ length: 3 }, (_, i) => ({
	const initialRows = Array.from({ length: 3 }, () => ({

[priyankeshh]

Suggested change

	const handleTableCellEdit = (cell: any) => {
	const handleTableCellEdit = (_cell: any) => {

[priyankeshh]

Suggested change

	const initialRows = Array.from({ length: 3 }, (_, i) => ({
	const initialRows = Array.from({ length: 3 }, () => ({