diff --git a/copilot_changes.txt b/copilot_changes.txt
new file mode 100644
index 000000000..4b8b510a2
--- /dev/null
+++ b/copilot_changes.txt
@@ -0,0 +1,824 @@
+diff --git a/extralit-frontend/components/base/base-render-table/RenderTable.vue b/extralit-frontend/components/base/base-render-table/RenderTable.vue
+index ff6874489..ab73e5afb 100644
+--- a/extralit-frontend/components/base/base-render-table/RenderTable.vue
++++ b/extralit-frontend/components/base/base-render-table/RenderTable.vue
+@@ -150,6 +150,7 @@ export default {
+ // }
+ // },
+ // },
++
+ validation: {
+ handler(newValidation, oldValidation) {
+ if (this.isLoaded) {
+@@ -196,7 +197,7 @@ export default {
+ var configs = this.tableJSON.schema.fields.map((column: DataFrameField) => {
+ const commonConfig = this.generateColumnConfig(column.name);
+ const editableConfig = this.generateColumnEditableConfig(column.name);
+- return { ...commonConfig, ...editableConfig };
++ return { ...commonConfig, ...editableConfig, ...column };
+ });
+
+ if (!this.editable) {
+@@ -913,6 +914,7 @@ export default {
+
+ this.tabulator.on("cellEdited", (cell: CellComponent) => {
+ this.updateTableJsonData();
++ this.$emit("cell-edited", cell);
+ // const rowPos: number | boolean = cell.getRow().getPosition();
+ // if (typeof rowPos != 'number' || rowPos < 0 || rowPos > this.tableJSON.data.length) return;
+ // this.$set(this.tableJSON.data[rowPos-1], cell.getColumn().getField(), cell.getValue());
+diff --git a/extralit-frontend/components/base/base-simple-table/BaseSimpleTable.vue b/extralit-frontend/components/base/base-simple-table/BaseSimpleTable.vue
+index 15a62bbc4..3a7e5435a 100644
+--- a/extralit-frontend/components/base/base-simple-table/BaseSimpleTable.vue
++++ b/extralit-frontend/components/base/base-simple-table/BaseSimpleTable.vue
+@@ -6,6 +6,7 @@
+ :editable="editable"
+ :hasValidValues="hasValidValues"
+ :questions="questions"
++ :validation="validation || validators"
+ @table-built="$emit('table-built')"
+ @row-click="(e, row) => $emit('row-click', e, row)"
+ @cell-edited="(cell) => $emit('cell-edited', cell)"
+@@ -71,9 +72,11 @@ export default {
+ computed: {
+ // Convert simple data/columns to TableData format for RenderTable
+ computedTableJSON(): TableData {
++ // FIX 1: Use "...col" to preserve editor config (dropdowns), validators, and freezing
+ const fields = this.columns.map((col: any) => ({
+ name: col.field,
+ type: col.type || "string",
++ ...col // <--- THIS IS THE MAGIC FIX
+ }));
+
+ const schema = new DataFrameSchema(
+@@ -89,7 +92,14 @@ export default {
+ null
+ );
+
+- if (this.validation) {
++ // FIX 2: Handle both 'validation' and 'validators' props
++ // ImportFileUpload passes :validators, so we must prioritize that.
++ if (this.validators) {
++ // We wrap it in a structure RenderTable understands
++ tableData.validation = { columns: {}, ...this.validation };
++ // We might need to pass this directly to the RenderTable prop instead,
++ // but attaching it to tableData is the safest way for the Schema to know about it.
++ } else if (this.validation) {
+ tableData.validation = this.validation;
+ }
+
+diff --git a/extralit-frontend/components/features/import/analysis/useImportAnalysisTableViewModel.ts b/extralit-frontend/components/features/import/analysis/useImportAnalysisTableViewModel.ts
+index 99eb2e8eb..825cd0a6a 100644
+--- a/extralit-frontend/components/features/import/analysis/useImportAnalysisTableViewModel.ts
++++ b/extralit-frontend/components/features/import/analysis/useImportAnalysisTableViewModel.ts
+@@ -98,6 +98,8 @@ export const useImportAnalysisTableViewModel = (props: {
+ workspaceId: props.workspace?.id,
+ dataframeLength: props.dataframeData?.data?.length,
+ matchedFilesLength: props.pdfData?.matchedFiles?.length,
++ // Add deep watch on dataframe data to catch cell edits
++ dataframeDataHash: props.dataframeData ? JSON.stringify(props.dataframeData.data) : null,
+ }),
+ (newVal, oldVal) => {
+ // Only trigger if we have all required data and something actually changed
+@@ -107,7 +109,8 @@ export const useImportAnalysisTableViewModel = (props: {
+ !oldVal ||
+ newVal.workspaceId !== oldVal.workspaceId ||
+ newVal.dataframeLength !== oldVal.dataframeLength ||
+- newVal.matchedFilesLength !== oldVal.matchedFilesLength
++ newVal.matchedFilesLength !== oldVal.matchedFilesLength ||
++ newVal.dataframeDataHash !== oldVal.dataframeDataHash
+ ) {
+ analyzeImport(props.workspace!, props.dataframeData!, props.pdfData!.matchedFiles);
+ }
+diff --git a/extralit-frontend/components/features/import/file-upload/ImportFileUpload.vue b/extralit-frontend/components/features/import/file-upload/ImportFileUpload.vue
+index 381d641e3..e594d8e90 100644
+--- a/extralit-frontend/components/features/import/file-upload/ImportFileUpload.vue
++++ b/extralit-frontend/components/features/import/file-upload/ImportFileUpload.vue
+@@ -12,6 +12,34 @@
+
+
+
++
++
++
++
++
++
++
++
++
++
Unmapped PDF Files ({{ unmappedPdfFiles.length }})
++
++
++
+
+
+
+@@ -24,6 +52,7 @@
+ import TableUpload from "./TableUpload.vue";
+ import PdfUpload from "./PdfUpload.vue";
+ import ImportSummarySidebar from "./ImportSummarySidebar.vue";
++ import BaseSimpleTable from "~/components/base/base-simple-table/BaseSimpleTable.vue";
+ import { useImportFileUploadViewModel } from "./useImportFileUploadViewModel";
+
+ export default {
+@@ -33,6 +62,7 @@
+ TableUpload,
+ PdfUpload,
+ ImportSummarySidebar,
++ BaseSimpleTable,
+ } as any,
+
+ props: {
+@@ -686,5 +716,68 @@
+ flex-direction: column;
+ }
+ }
++
++ // Editable Table Styles
++ &__editable-table {
++ display: flex;
++ flex-direction: column;
++ gap: $base-space * 2;
++ padding: $base-space * 3;
++ background: var(--bg-accent-grey-1);
++ border: 1px solid var(--border-field);
++ border-radius: $border-radius-m;
++ }
++
++ &__editable-table-header {
++ margin-bottom: $base-space;
++
++ .import-file-upload__section-title {
++ font-size: 1.2rem;
++ font-weight: 600;
++ margin-bottom: $base-space;
++ color: var(--fg-primary);
++ }
++
++ .import-file-upload__section-description {
++ color: var(--fg-secondary);
++ font-size: 0.9rem;
++ margin-bottom: 0;
++ line-height: 1.4;
++
++ strong {
++ color: var(--fg-primary);
++ font-weight: 600;
++ }
++ }
++ }
++
++ &__unmapped-pdfs {
++ margin-top: $base-space * 2;
++ padding: $base-space * 2;
++ background: var(--bg-banner-warning);
++ border: 1px solid var(--color-warning);
++ border-radius: $border-radius;
++
++ h4 {
++ margin: 0 0 $base-space 0;
++ color: var(--fg-primary);
++ font-size: 1rem;
++ font-weight: 600;
++ }
++
++ .unmapped-files-list {
++ margin: 0;
++ padding-left: $base-space * 3;
++ max-height: 200px;
++ overflow-y: auto;
++
++ li {
++ color: var(--fg-primary);
++ font-size: 0.9rem;
++ margin-bottom: calc($base-space / 2);
++ font-family: $quaternary-font-family;
++ }
++ }
++ }
+ }
+
+diff --git a/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.spec.ts b/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.spec.ts
+new file mode 100644
+index 000000000..9cefe37c8
+--- /dev/null
++++ b/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.spec.ts
+@@ -0,0 +1,201 @@
++import { ref } from "@nuxtjs/composition-api";
++import { useImportFileUploadViewModel } from "./useImportFileUploadViewModel";
++
++// Mock the dependencies
++jest.mock("ts-injecty", () => ({
++ useResolve: jest.fn(),
++}));
++
++jest.mock("~/v1/domain/entities/table/TableData", () => ({
++ TableData: jest.fn().mockImplementation((data, schema, validation) => ({
++ data,
++ schema,
++ validation,
++ })),
++}));
++
++jest.mock("~/v1/domain/entities/table/Schema", () => ({
++ DataFrameSchema: jest.fn().mockImplementation((fields, primaryKey, foreignKeys, name) => ({
++ fields,
++ primaryKey,
++ foreignKeys,
++ name,
++ })),
++ DataFrameField: jest.fn(),
++}));
++
++jest.mock("~/v1/domain/entities/table/Validation", () => ({
++ Validators: jest.fn(),
++}));
++
++describe("useImportFileUploadViewModel", () => {
++ let emit: jest.Mock;
++ let props: any;
++
++ beforeEach(() => {
++ emit = jest.fn();
++ props = {
++ initialBibData: {
++ fileName: "",
++ dataframeData: null,
++ rawContent: "",
++ },
++ initialPdfData: {
++ matchedFiles: [],
++ unmatchedFiles: [],
++ totalFiles: 0,
++ },
++ };
++ });
++
++ describe("shouldShowEditableTable", () => {
++ it("should return true when PDFs are uploaded but no bibliography", () => {
++ const viewModel = useImportFileUploadViewModel(props, { emit });
++
++ // Simulate PDF upload
++ viewModel.handlePdfUpdate({
++ matchedFiles: [],
++ unmatchedFiles: [{ name: "test.pdf" }],
++ totalFiles: 1,
++ });
++
++ expect(viewModel.shouldShowEditableTable.value).toBe(true);
++ });
++
++ it("should return false when no PDFs are uploaded", () => {
++ const viewModel = useImportFileUploadViewModel(props, { emit });
++
++ expect(viewModel.shouldShowEditableTable.value).toBe(false);
++ });
++
++ it("should return false when bibliography is uploaded", () => {
++ const viewModel = useImportFileUploadViewModel(props, { emit });
++
++ // Simulate PDF upload
++ viewModel.handlePdfUpdate({
++ matchedFiles: [],
++ unmatchedFiles: [{ name: "test.pdf" }],
++ totalFiles: 1,
++ });
++
++ // Simulate bibliography upload
++ viewModel.handleBibUpdate({
++ fileName: "test.bib",
++ dataframeData: {
++ data: [{ reference: "test2023", title: "Test Paper" }],
++ schema: {},
++ },
++ rawContent: "",
++ });
++
++ expect(viewModel.shouldShowEditableTable.value).toBe(false);
++ });
++ });
++
++ describe("editableTableColumns", () => {
++ it("should include reference and files columns with proper configuration", () => {
++ const viewModel = useImportFileUploadViewModel(props, { emit });
++
++ // Simulate PDF upload
++ viewModel.handlePdfUpdate({
++ matchedFiles: [],
++ unmatchedFiles: [{ name: "test1.pdf" }, { name: "test2.pdf" }],
++ totalFiles: 2,
++ });
++
++ const columns = viewModel.editableTableColumns.value;
++ const referenceCol = columns.find((col: any) => col.field === "reference");
++ const filesCol = columns.find((col: any) => col.field === "files");
++
++ expect(referenceCol).toBeDefined();
++ expect(referenceCol?.frozen).toBe(true);
++ expect(referenceCol?.validator).toContain("required");
++ expect(referenceCol?.validator).toContain("unique");
++
++ expect(filesCol).toBeDefined();
++ expect(filesCol?.editor).toBe("list");
++ expect(filesCol?.editorParams?.multiselect).toBe(true);
++ expect(filesCol?.editorParams?.values).toHaveLength(2);
++ });
++ });
++
++ describe("unmappedPdfFiles", () => {
++ it("should return all PDFs when no files are assigned", () => {
++ const viewModel = useImportFileUploadViewModel(props, { emit });
++
++ viewModel.handlePdfUpdate({
++ matchedFiles: [],
++ unmatchedFiles: [{ name: "test1.pdf" }, { name: "test2.pdf" }],
++ totalFiles: 2,
++ });
++
++ expect(viewModel.unmappedPdfFiles.value).toEqual(["test1.pdf", "test2.pdf"]);
++ });
++
++ it("should exclude assigned PDFs from unmapped list", () => {
++ const viewModel = useImportFileUploadViewModel(props, { emit });
++
++ viewModel.handlePdfUpdate({
++ matchedFiles: [],
++ unmatchedFiles: [{ name: "test1.pdf" }, { name: "test2.pdf" }],
++ totalFiles: 2,
++ });
++
++ // Manually set table data with one assigned file
++ viewModel.editableTableData.value = [
++ {
++ reference: "test2023",
++ files: ["test1.pdf"],
++ },
++ ];
++
++ expect(viewModel.unmappedPdfFiles.value).toEqual(["test2.pdf"]);
++ });
++ });
++
++ describe("syncEditableTableToBibData", () => {
++ it("should convert editable table data to bibData format", () => {
++ const viewModel = useImportFileUploadViewModel(props, { emit });
++
++ viewModel.editableTableData.value = [
++ {
++ reference: "test2023",
++ title: "Test Paper",
++ authors: "John Doe",
++ year: "2023",
++ files: ["test.pdf"],
++ },
++ ];
++
++ viewModel.syncEditableTableToBibData();
++
++ expect(viewModel.bibData.value.dataframeData).toBeDefined();
++ expect(viewModel.bibData.value.dataframeData?.data).toHaveLength(1);
++ expect(viewModel.bibData.value.dataframeData?.data[0]).toHaveProperty("reference", "test2023");
++ expect(viewModel.bibData.value.dataframeData?.data[0]).toHaveProperty("filePaths");
++ expect(viewModel.bibData.value.dataframeData?.data[0].filePaths).toEqual(["test.pdf"]);
++ });
++
++ it("should filter out empty rows", () => {
++ const viewModel = useImportFileUploadViewModel(props, { emit });
++
++ viewModel.editableTableData.value = [
++ {
++ reference: "test2023",
++ title: "Test Paper",
++ files: ["test.pdf"],
++ },
++ {
++ reference: "",
++ title: "",
++ files: [],
++ },
++ ];
++
++ viewModel.syncEditableTableToBibData();
++
++ expect(viewModel.bibData.value.dataframeData).toBeDefined();
++ expect(viewModel.bibData.value.dataframeData?.data).toHaveLength(1);
++ });
++ });
++});
+diff --git a/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.ts b/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.ts
+index 1ebb8a8ca..e3833ca1f 100644
+--- a/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.ts
++++ b/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.ts
+@@ -5,6 +5,9 @@
+
+ import { ref, computed, watch, nextTick } from "@nuxtjs/composition-api";
+ import type { BibliographyData, PdfData } from "./types";
++import { TableData } from "~/v1/domain/entities/table/TableData";
++import { DataFrameSchema, DataFrameField } from "~/v1/domain/entities/table/Schema";
++import { Validators } from "~/v1/domain/entities/table/Validation";
+
+ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
+ // Internal flag to prevent recursive updates during initialization
+@@ -23,12 +26,179 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
+ unmatchedFiles: [],
+ totalFiles: 0,
+ });
++ const hasAutoSubmitted = ref(false);
++
++ // Editable table data for PDF-only uploads
++ const editableTableData = ref([]);
++ const editableTable = ref(null);
+
+ // Computed properties
+ const isValid = computed(() => {
+ return pdfData.value.totalFiles > 0;
+ });
+
++ // Check if we should show the editable table (PDFs uploaded but no bibliography)
++ const shouldShowEditableTable = computed(() => {
++ const hasPdfs = pdfData.value.totalFiles > 0;
++ const noBibliography = !bibData.value.dataframeData || bibData.value.dataframeData.data.length === 0;
++ return hasPdfs && noBibliography;
++ });
++
++ // Get all PDF file names
++ const allPdfFileNames = computed(() => {
++ const matched = pdfData.value.matchedFiles.map((mf: any) => mf.file.name);
++ const unmatched = pdfData.value.unmatchedFiles.map((f: File) => f.name);
++ return [...matched, ...unmatched];
++ });
++
++ // Get unmapped PDF files (PDFs not assigned to any reference)
++ const unmappedPdfFiles = computed(() => {
++ const assignedFiles = new Set();
++
++ // π Prefer Tabulator ONLY when ready
++ const rows = editableTable.value
++ ? editableTable.value.getData()
++ : editableTableData.value;
++
++ rows.forEach((row: any) => {
++ // π Ignore empty rows
++ if (!row.reference || !row.reference.trim()) return;
++
++ if (!row.files) return;
++ (Array.isArray(row.files) ? row.files : [row.files]).forEach(
++ (file: string) => assignedFiles.add(file)
++ );
++ });
++
++
++ return allPdfFileNames.value.filter(
++ fileName => !assignedFiles.has(fileName)
++ );
++ });
++
++
++
++ // Configure editable table columns with validators
++ const editableTableColumns = computed(() => {
++ const pdfFileOptions = allPdfFileNames.value.map(name => ({
++ label: name,
++ value: name,
++ }));
++
++ return [
++ {
++ field: "reference",
++ title: "Reference *",
++ frozen: true,
++ width: 200,
++ editor: "input",
++ validator: ["required", "unique"],
++ },
++ {
++ field: "title",
++ title: "Title",
++ width: 300,
++ editor: "input",
++ },
++ {
++ field: "authors",
++ title: "Authors",
++ width: 200,
++ editor: "input",
++ },
++ {
++ field: "year",
++ title: "Year",
++ width: 100,
++ editor: "input",
++ },
++ {
++ field: "journal",
++ title: "Journal",
++ width: 200,
++ editor: "input",
++ },
++ {
++ field: "doi",
++ title: "DOI",
++ width: 150,
++ editor: "input",
++ },
++ {
++ field: "files",
++ title: "Files *",
++ frozen: true,
++ frozenRight: true,
++ width: 200,
++ editor: "list",
++
++ editorParams: function (cell: any) {
++ const table = cell.getTable();
++ const row = cell.getRow();
++ const field = cell.getField();
++
++ // β
Source of truth: uploaded PDFs
++ const allFiles = new Set(allPdfFileNames.value);
++
++ // β
Files already used in other rows
++ const usedFiles = new Set();
++
++ table.getRows().forEach((r: any) => {
++ if (r === row) return;
++ const v = r.getData()[field];
++ if (!v) return;
++ (Array.isArray(v) ? v : [v]).forEach((f: string) =>
++ usedFiles.add(f)
++ );
++ });
++
++ // β
Allow current row selections
++ const current = cell.getValue() || [];
++ const currentSet = new Set(
++ Array.isArray(current) ? current : [current]
++ );
++
++ // β
Compute final list AT CLICK TIME
++ const values = [...allFiles]
++ .filter(f => !usedFiles.has(f) || currentSet.has(f))
++ .map(f => ({ label: f, value: f }));
++
++ return {
++ values,
++ multiselect: true,
++ autocomplete: false,
++ listOnEmpty: true,
++ clearable: true,
++ };
++ },
++
++ validator: ["required"],
++
++ formatter: (cell: any) => {
++ const value = cell.getValue();
++ if (!value || (Array.isArray(value) && value.length === 0)) {
++ return 'No files ';
++ }
++ const files = Array.isArray(value) ? value : [value];
++ const count = files.length;
++ return `${count} file${count !== 1 ? 's' : ''} `;
++ },
++ }
++
++ ];
++ });
++
++ // Validators for the editable table
++ const editableTableValidators = computed(() => {
++ return {
++ reference: [
++ { type: "unique", parameters: { column: "reference" } },
++ "required",
++ ],
++ files: ["required"],
++ };
++ });
++
+ // Event handlers
+ const handleBibUpdate = (data: any) => {
+ bibData.value = {
+@@ -36,22 +206,49 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
+ dataframeData: data.dataframeData || null,
+ rawContent: data.rawContent || "",
+ };
++
++ // If a bibliography is uploaded, clear the editable table data
++ if (data.dataframeData && data.dataframeData.data && data.dataframeData.data.length > 0) {
++ editableTableData.value = [];
++ }
++
+ emitBibUpdate();
+ };
+
+ const handlePdfUpdate = (data: any) => {
++ hasAutoSubmitted.value = false;
+ pdfData.value = {
+ matchedFiles: data.matchedFiles || [],
+ unmatchedFiles: data.unmatchedFiles || [],
+ totalFiles: data.totalFiles || 0,
+ };
+
++ // Initialize editable table if needed (PDFs but no bib)
++ if (shouldShowEditableTable.value && editableTableData.value.length === 0) {
++ initializeEditableTable();
++ }
++
+ // Update dataframe data with matched file paths
+ updateDataframeWithFilePaths(data.matchedFiles || []);
+
+ emitPdfUpdate();
+ };
+
++ const handleTableCellEdit = (cell: any) => {
++ // Keep Vue mirror in sync ONLY
++ editableTableData.value = editableTable.value?.getData() || [];
++ };
++
++ const handleTableBuilt = () => {
++ // Table is ready, ensure data is in sync
++ if (editableTable.value) {
++ const tableData = editableTable.value.getData();
++ if (tableData && tableData.length > 0) {
++ editableTableData.value = tableData;
++ }
++ }
++ };
++
+ // Event emitters
+ const emitBibUpdate = () => {
+ emit("bib-update", {
+@@ -118,6 +315,86 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
+ emitBibUpdate();
+ };
+
++ // Initialize editable table with empty rows
++ const initializeEditableTable = () => {
++ // Start with a few empty rows
++ const initialRows = Array.from({ length: 3 }, (_, i) => ({
++ reference: "",
++ title: "",
++ authors: "",
++ year: "",
++ journal: "",
++ doi: "",
++ files: [],
++ }));
++
++ editableTableData.value = initialRows;
++ };
++
++ // Sync editable table data to bibData format
++ // Sync editable table data to bibData format
++ const syncEditableTableToBibData = () => {
++ if (editableTableData.value.length === 0) {
++ return;
++ }
++
++ // Filter out empty rows
++ const validRows = editableTableData.value.filter((row: any) =>
++ row.reference && row.reference.trim().length > 0
++ );
++
++ if (validRows.length === 0) {
++ return;
++ }
++
++ // Define schema
++ const fields: DataFrameField[] = [
++ { name: "reference", type: "string" },
++ { name: "title", type: "string" },
++ { name: "authors", type: "string" },
++ { name: "year", type: "string" },
++ { name: "journal", type: "string" },
++ { name: "doi", type: "string" },
++ { name: "files", type: "string" },
++ ];
++
++ const schema = new DataFrameSchema(
++ fields,
++ ["reference"],
++ null,
++ "manual-entry"
++ );
++
++ // Process rows: Format 'files' for compatibility
++ const processedRows = validRows.map((row: any) => {
++ // 1. Normalize files to an Array (Safe handling)
++ const filesArray = Array.isArray(row.files) ? row.files : (row.files ? [row.files] : []);
++
++ return {
++ ...row,
++ // 2. THE FIX: Convert Array back to String for Step 2 display
++ // Step 2 expects "file1.pdf, file2.pdf" and tries to .split() it.
++ // We give it exactly what it wants.
++ files: filesArray.join(', '),
++
++ // 3. Keep the real Array for the backend logic
++ filePaths: filesArray,
++ };
++ });
++
++ const tableData = new TableData(
++ processedRows,
++ schema,
++ null
++ );
++
++ bibData.value.dataframeData = tableData;
++ bibData.value.fileName = "manual-entry.csv";
++
++ // Re-emit the bib update with the generated dataframe
++ emitBibUpdate();
++ };
++
+ // Initialize component with existing data when navigating back
+ const initializeWithExistingData = () => {
+ // Set flag to prevent recursive updates
+@@ -154,7 +431,7 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
+ const reset = () => {
+ // Set flag to prevent recursive updates during reset
+ isInitializing.value = true;
+-
++ hasAutoSubmitted.value = false;
+ // Reset bibliography data
+ bibData.value = {
+ fileName: "",
+@@ -162,6 +439,7 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
+ rawContent: "",
+ };
+
++
+ // Reset PDF data
+ pdfData.value = {
+ matchedFiles: [],
+@@ -215,21 +493,52 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
+ { deep: true, immediate: true }
+ );
+
++ watch(
++ unmappedPdfFiles,
++ (newUnmapped) => {
++ // Only auto-submit when:
++ // 1. Table exists
++ // 2. No unmapped PDFs remain
++ // 3. We haven't already submitted
++ if (
++ editableTable.value &&
++ newUnmapped.length === 0 &&
++ !hasAutoSubmitted.value
++ ) {
++ hasAutoSubmitted.value = true;
++ syncEditableTableToBibData();
++ }
++ },
++ { immediate: false }
++ );
++
++
+ return {
+ // Reactive state
+ isInitializing,
+ bibData,
+ pdfData,
++ editableTableData,
++ editableTable,
+
+ // Computed
+ isValid,
++ shouldShowEditableTable,
++ allPdfFileNames,
++ unmappedPdfFiles,
++ editableTableColumns,
++ editableTableValidators,
+
+ // Methods
+ handleBibUpdate,
+ handlePdfUpdate,
++ handleTableCellEdit,
++ handleTableBuilt,
+ emitBibUpdate,
+ emitPdfUpdate,
+ updateDataframeWithFilePaths,
++ initializeEditableTable,
++ syncEditableTableToBibData,
+ initializeWithExistingData,
+ reset,
+ };
diff --git a/extralit-frontend/components/features/import/file-upload/ImportFileUpload.vue b/extralit-frontend/components/features/import/file-upload/ImportFileUpload.vue
index c426a4ca3..eabc68b3e 100644
--- a/extralit-frontend/components/features/import/file-upload/ImportFileUpload.vue
+++ b/extralit-frontend/components/features/import/file-upload/ImportFileUpload.vue
@@ -25,6 +25,7 @@
import TableUpload from "./TableUpload.vue";
import PdfUpload from "./PdfUpload.vue";
import ImportSummarySidebar from "./ImportSummarySidebar.vue";
+ import BaseSimpleTable from "~/components/base/base-simple-table/BaseSimpleTable.vue";
import { useImportFileUploadViewModel } from "./useImportFileUploadViewModel";
export default {
@@ -34,6 +35,7 @@
TableUpload,
PdfUpload,
ImportSummarySidebar,
+ BaseSimpleTable,
} as any,
props: {
diff --git a/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.spec.ts b/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.spec.ts
new file mode 100644
index 000000000..9cefe37c8
--- /dev/null
+++ b/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.spec.ts
@@ -0,0 +1,201 @@
+import { ref } from "@nuxtjs/composition-api";
+import { useImportFileUploadViewModel } from "./useImportFileUploadViewModel";
+
+// Mock the dependencies
+jest.mock("ts-injecty", () => ({
+ useResolve: jest.fn(),
+}));
+
+jest.mock("~/v1/domain/entities/table/TableData", () => ({
+ TableData: jest.fn().mockImplementation((data, schema, validation) => ({
+ data,
+ schema,
+ validation,
+ })),
+}));
+
+jest.mock("~/v1/domain/entities/table/Schema", () => ({
+ DataFrameSchema: jest.fn().mockImplementation((fields, primaryKey, foreignKeys, name) => ({
+ fields,
+ primaryKey,
+ foreignKeys,
+ name,
+ })),
+ DataFrameField: jest.fn(),
+}));
+
+jest.mock("~/v1/domain/entities/table/Validation", () => ({
+ Validators: jest.fn(),
+}));
+
+describe("useImportFileUploadViewModel", () => {
+ let emit: jest.Mock;
+ let props: any;
+
+ beforeEach(() => {
+ emit = jest.fn();
+ props = {
+ initialBibData: {
+ fileName: "",
+ dataframeData: null,
+ rawContent: "",
+ },
+ initialPdfData: {
+ matchedFiles: [],
+ unmatchedFiles: [],
+ totalFiles: 0,
+ },
+ };
+ });
+
+ describe("shouldShowEditableTable", () => {
+ it("should return true when PDFs are uploaded but no bibliography", () => {
+ const viewModel = useImportFileUploadViewModel(props, { emit });
+
+ // Simulate PDF upload
+ viewModel.handlePdfUpdate({
+ matchedFiles: [],
+ unmatchedFiles: [{ name: "test.pdf" }],
+ totalFiles: 1,
+ });
+
+ expect(viewModel.shouldShowEditableTable.value).toBe(true);
+ });
+
+ it("should return false when no PDFs are uploaded", () => {
+ const viewModel = useImportFileUploadViewModel(props, { emit });
+
+ expect(viewModel.shouldShowEditableTable.value).toBe(false);
+ });
+
+ it("should return false when bibliography is uploaded", () => {
+ const viewModel = useImportFileUploadViewModel(props, { emit });
+
+ // Simulate PDF upload
+ viewModel.handlePdfUpdate({
+ matchedFiles: [],
+ unmatchedFiles: [{ name: "test.pdf" }],
+ totalFiles: 1,
+ });
+
+ // Simulate bibliography upload
+ viewModel.handleBibUpdate({
+ fileName: "test.bib",
+ dataframeData: {
+ data: [{ reference: "test2023", title: "Test Paper" }],
+ schema: {},
+ },
+ rawContent: "",
+ });
+
+ expect(viewModel.shouldShowEditableTable.value).toBe(false);
+ });
+ });
+
+ describe("editableTableColumns", () => {
+ it("should include reference and files columns with proper configuration", () => {
+ const viewModel = useImportFileUploadViewModel(props, { emit });
+
+ // Simulate PDF upload
+ viewModel.handlePdfUpdate({
+ matchedFiles: [],
+ unmatchedFiles: [{ name: "test1.pdf" }, { name: "test2.pdf" }],
+ totalFiles: 2,
+ });
+
+ const columns = viewModel.editableTableColumns.value;
+ const referenceCol = columns.find((col: any) => col.field === "reference");
+ const filesCol = columns.find((col: any) => col.field === "files");
+
+ expect(referenceCol).toBeDefined();
+ expect(referenceCol?.frozen).toBe(true);
+ expect(referenceCol?.validator).toContain("required");
+ expect(referenceCol?.validator).toContain("unique");
+
+ expect(filesCol).toBeDefined();
+ expect(filesCol?.editor).toBe("list");
+ expect(filesCol?.editorParams?.multiselect).toBe(true);
+ expect(filesCol?.editorParams?.values).toHaveLength(2);
+ });
+ });
+
+ describe("unmappedPdfFiles", () => {
+ it("should return all PDFs when no files are assigned", () => {
+ const viewModel = useImportFileUploadViewModel(props, { emit });
+
+ viewModel.handlePdfUpdate({
+ matchedFiles: [],
+ unmatchedFiles: [{ name: "test1.pdf" }, { name: "test2.pdf" }],
+ totalFiles: 2,
+ });
+
+ expect(viewModel.unmappedPdfFiles.value).toEqual(["test1.pdf", "test2.pdf"]);
+ });
+
+ it("should exclude assigned PDFs from unmapped list", () => {
+ const viewModel = useImportFileUploadViewModel(props, { emit });
+
+ viewModel.handlePdfUpdate({
+ matchedFiles: [],
+ unmatchedFiles: [{ name: "test1.pdf" }, { name: "test2.pdf" }],
+ totalFiles: 2,
+ });
+
+ // Manually set table data with one assigned file
+ viewModel.editableTableData.value = [
+ {
+ reference: "test2023",
+ files: ["test1.pdf"],
+ },
+ ];
+
+ expect(viewModel.unmappedPdfFiles.value).toEqual(["test2.pdf"]);
+ });
+ });
+
+ describe("syncEditableTableToBibData", () => {
+ it("should convert editable table data to bibData format", () => {
+ const viewModel = useImportFileUploadViewModel(props, { emit });
+
+ viewModel.editableTableData.value = [
+ {
+ reference: "test2023",
+ title: "Test Paper",
+ authors: "John Doe",
+ year: "2023",
+ files: ["test.pdf"],
+ },
+ ];
+
+ viewModel.syncEditableTableToBibData();
+
+ expect(viewModel.bibData.value.dataframeData).toBeDefined();
+ expect(viewModel.bibData.value.dataframeData?.data).toHaveLength(1);
+ expect(viewModel.bibData.value.dataframeData?.data[0]).toHaveProperty("reference", "test2023");
+ expect(viewModel.bibData.value.dataframeData?.data[0]).toHaveProperty("filePaths");
+ expect(viewModel.bibData.value.dataframeData?.data[0].filePaths).toEqual(["test.pdf"]);
+ });
+
+ it("should filter out empty rows", () => {
+ const viewModel = useImportFileUploadViewModel(props, { emit });
+
+ viewModel.editableTableData.value = [
+ {
+ reference: "test2023",
+ title: "Test Paper",
+ files: ["test.pdf"],
+ },
+ {
+ reference: "",
+ title: "",
+ files: [],
+ },
+ ];
+
+ viewModel.syncEditableTableToBibData();
+
+ expect(viewModel.bibData.value.dataframeData).toBeDefined();
+ expect(viewModel.bibData.value.dataframeData?.data).toHaveLength(1);
+ });
+ });
+});
diff --git a/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.ts b/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.ts
index aa0cdfec1..8c9d05bea 100644
--- a/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.ts
+++ b/extralit-frontend/components/features/import/file-upload/useImportFileUploadViewModel.ts
@@ -5,6 +5,9 @@
import { ref, computed, watch, nextTick } from "@nuxtjs/composition-api";
import type { BibliographyData, PdfData } from "./types";
+import { TableData } from "~/v1/domain/entities/table/TableData";
+import { DataFrameSchema, DataFrameField } from "~/v1/domain/entities/table/Schema";
+import { Validators } from "~/v1/domain/entities/table/Validation";
export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
// Internal flag to prevent recursive updates during initialization
@@ -23,12 +26,179 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
unmatchedFiles: [],
totalFiles: 0,
});
+ const hasAutoSubmitted = ref(false);
+
+ // Editable table data for PDF-only uploads
+ const editableTableData = ref([]);
+ const editableTable = ref(null);
// Computed properties
const isValid = computed(() => {
return pdfData.value.totalFiles > 0;
});
+ // Check if we should show the editable table (PDFs uploaded but no bibliography)
+ const shouldShowEditableTable = computed(() => {
+ const hasPdfs = pdfData.value.totalFiles > 0;
+ const noBibliography = !bibData.value.dataframeData || bibData.value.dataframeData.data.length === 0;
+ return hasPdfs && noBibliography;
+ });
+
+ // Get all PDF file names
+ const allPdfFileNames = computed(() => {
+ const matched = pdfData.value.matchedFiles.map((mf: any) => mf.file.name);
+ const unmatched = pdfData.value.unmatchedFiles.map((f: File) => f.name);
+ return [...matched, ...unmatched];
+ });
+
+ // Get unmapped PDF files (PDFs not assigned to any reference)
+ const unmappedPdfFiles = computed(() => {
+ const assignedFiles = new Set();
+
+ // π Prefer Tabulator ONLY when ready
+ const rows = editableTable.value
+ ? editableTable.value.getData()
+ : editableTableData.value;
+
+ rows.forEach((row: any) => {
+ // π Ignore empty rows
+ if (!row.reference || !row.reference.trim()) return;
+
+ if (!row.files) return;
+ (Array.isArray(row.files) ? row.files : [row.files]).forEach(
+ (file: string) => assignedFiles.add(file)
+ );
+ });
+
+
+ return allPdfFileNames.value.filter(
+ fileName => !assignedFiles.has(fileName)
+ );
+ });
+
+
+
+ // Configure editable table columns with validators
+ const editableTableColumns = computed(() => {
+ const pdfFileOptions = allPdfFileNames.value.map(name => ({
+ label: name,
+ value: name,
+ }));
+
+ return [
+ {
+ field: "reference",
+ title: "Reference *",
+ frozen: true,
+ width: 200,
+ editor: "input",
+ validator: ["required", "unique"],
+ },
+ {
+ field: "title",
+ title: "Title",
+ width: 300,
+ editor: "input",
+ },
+ {
+ field: "authors",
+ title: "Authors",
+ width: 200,
+ editor: "input",
+ },
+ {
+ field: "year",
+ title: "Year",
+ width: 100,
+ editor: "input",
+ },
+ {
+ field: "journal",
+ title: "Journal",
+ width: 200,
+ editor: "input",
+ },
+ {
+ field: "doi",
+ title: "DOI",
+ width: 150,
+ editor: "input",
+ },
+ {
+ field: "files",
+ title: "Files *",
+ frozen: true,
+ frozenRight: true,
+ width: 200,
+ editor: "list",
+
+ editorParams: function (cell: any) {
+ const table = cell.getTable();
+ const row = cell.getRow();
+ const field = cell.getField();
+
+ // β
Source of truth: uploaded PDFs
+ const allFiles = new Set(allPdfFileNames.value);
+
+ // β
Files already used in other rows
+ const usedFiles = new Set();
+
+ table.getRows().forEach((r: any) => {
+ if (r === row) return;
+ const v = r.getData()[field];
+ if (!v) return;
+ (Array.isArray(v) ? v : [v]).forEach((f: string) =>
+ usedFiles.add(f)
+ );
+ });
+
+ // β
Allow current row selections
+ const current = cell.getValue() || [];
+ const currentSet = new Set(
+ Array.isArray(current) ? current : [current]
+ );
+
+ // β
Compute final list AT CLICK TIME
+ const values = [...allFiles]
+ .filter(f => !usedFiles.has(f) || currentSet.has(f))
+ .map(f => ({ label: f, value: f }));
+
+ return {
+ values,
+ multiselect: true,
+ autocomplete: false,
+ listOnEmpty: true,
+ clearable: true,
+ };
+ },
+
+ validator: ["required"],
+
+ formatter: (cell: any) => {
+ const value = cell.getValue();
+ if (!value || (Array.isArray(value) && value.length === 0)) {
+ return 'No files ';
+ }
+ const files = Array.isArray(value) ? value : [value];
+ const count = files.length;
+ return `${count} file${count !== 1 ? 's' : ''} `;
+ },
+ }
+
+ ];
+ });
+
+ // Validators for the editable table
+ const editableTableValidators = computed(() => {
+ return {
+ reference: [
+ { type: "unique", parameters: { column: "reference" } },
+ "required",
+ ],
+ files: ["required"],
+ };
+ });
+
// Event handlers
const handleBibUpdate = (data: any) => {
bibData.value = {
@@ -41,18 +211,39 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
};
const handlePdfUpdate = (data: any) => {
+ hasAutoSubmitted.value = false;
pdfData.value = {
matchedFiles: data.matchedFiles || [],
unmatchedFiles: data.unmatchedFiles || [],
totalFiles: data.totalFiles || 0,
};
+ // Initialize editable table if needed (PDFs but no bib)
+ if (shouldShowEditableTable.value && editableTableData.value.length === 0) {
+ initializeEditableTable();
+ }
+
// Update dataframe data with matched file paths
updateDataframeWithFilePaths(data.matchedFiles || []);
emitPdfUpdate();
};
+ const handleTableCellEdit = (cell: any) => {
+ // Keep Vue mirror in sync ONLY
+ editableTableData.value = editableTable.value?.getData() || [];
+ };
+
+ const handleTableBuilt = () => {
+ // Table is ready, ensure data is in sync
+ if (editableTable.value) {
+ const tableData = editableTable.value.getData();
+ if (tableData && tableData.length > 0) {
+ editableTableData.value = tableData;
+ }
+ }
+ };
+
// Event emitters
const emitBibUpdate = () => {
emit("bib-update", {
@@ -119,6 +310,86 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
emitBibUpdate();
};
+ // Initialize editable table with empty rows
+ const initializeEditableTable = () => {
+ // Start with a few empty rows
+ const initialRows = Array.from({ length: 3 }, (_, i) => ({
+ reference: "",
+ title: "",
+ authors: "",
+ year: "",
+ journal: "",
+ doi: "",
+ files: [],
+ }));
+
+ editableTableData.value = initialRows;
+ };
+
+ // Sync editable table data to bibData format
+ // Sync editable table data to bibData format
+ const syncEditableTableToBibData = () => {
+ if (editableTableData.value.length === 0) {
+ return;
+ }
+
+ // Filter out empty rows
+ const validRows = editableTableData.value.filter((row: any) =>
+ row.reference && row.reference.trim().length > 0
+ );
+
+ if (validRows.length === 0) {
+ return;
+ }
+
+ // Define schema
+ const fields: DataFrameField[] = [
+ { name: "reference", type: "string" },
+ { name: "title", type: "string" },
+ { name: "authors", type: "string" },
+ { name: "year", type: "string" },
+ { name: "journal", type: "string" },
+ { name: "doi", type: "string" },
+ { name: "files", type: "string" },
+ ];
+
+ const schema = new DataFrameSchema(
+ fields,
+ ["reference"],
+ null,
+ "manual-entry"
+ );
+
+ // Process rows: Format 'files' for compatibility
+ const processedRows = validRows.map((row: any) => {
+ // 1. Normalize files to an Array (Safe handling)
+ const filesArray = Array.isArray(row.files) ? row.files : (row.files ? [row.files] : []);
+
+ return {
+ ...row,
+ // 2. THE FIX: Convert Array back to String for Step 2 display
+ // Step 2 expects "file1.pdf, file2.pdf" and tries to .split() it.
+ // We give it exactly what it wants.
+ files: filesArray.join(', '),
+
+ // 3. Keep the real Array for the backend logic
+ filePaths: filesArray,
+ };
+ });
+
+ const tableData = new TableData(
+ processedRows,
+ schema,
+ null
+ );
+
+ bibData.value.dataframeData = tableData;
+ bibData.value.fileName = "manual-entry.csv";
+
+ // Re-emit the bib update with the generated dataframe
+ emitBibUpdate();
+ };
+
// Initialize component with existing data when navigating back
const initializeWithExistingData = () => {
// Set flag to prevent recursive updates
@@ -155,7 +426,7 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
const reset = () => {
// Set flag to prevent recursive updates during reset
isInitializing.value = true;
-
+ hasAutoSubmitted.value = false;
// Reset bibliography data
bibData.value = {
fileName: "",
@@ -163,6 +434,7 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
rawContent: "",
};
+
// Reset PDF data
pdfData.value = {
matchedFiles: [],
@@ -216,21 +488,52 @@ export const useImportFileUploadViewModel = (props: any, { emit }: any) => {
{ deep: true, immediate: true }
);
+ watch(
+ unmappedPdfFiles,
+ (newUnmapped) => {
+ // Only auto-submit when:
+ // 1. Table exists
+ // 2. No unmapped PDFs remain
+ // 3. We haven't already submitted
+ if (
+ editableTable.value &&
+ newUnmapped.length === 0 &&
+ !hasAutoSubmitted.value
+ ) {
+ hasAutoSubmitted.value = true;
+ syncEditableTableToBibData();
+ }
+ },
+ { immediate: false }
+ );
+
+
return {
// Reactive state
isInitializing,
bibData,
pdfData,
+ editableTableData,
+ editableTable,
// Computed
isValid,
+ shouldShowEditableTable,
+ allPdfFileNames,
+ unmappedPdfFiles,
+ editableTableColumns,
+ editableTableValidators,
// Methods
handleBibUpdate,
handlePdfUpdate,
+ handleTableCellEdit,
+ handleTableBuilt,
emitBibUpdate,
emitPdfUpdate,
updateDataframeWithFilePaths,
+ initializeEditableTable,
+ syncEditableTableToBibData,
initializeWithExistingData,
reset,
};
diff --git a/extralit-frontend/components/features/user-settings/CopilotConnect.vue b/extralit-frontend/components/features/user-settings/CopilotConnect.vue
new file mode 100644
index 000000000..d043d08d4
--- /dev/null
+++ b/extralit-frontend/components/features/user-settings/CopilotConnect.vue
@@ -0,0 +1,179 @@
+
+
+
+
+ β
+ GitHub Copilot Connected
+
+
+
+
+
+
+
+ Waiting for authorizationβ¦
+
+
+
+
+
+
+ Connect Copilot
+
+
+
+
+
+
+
+
diff --git a/extralit-frontend/components/features/user-settings/UserSettingsContent.vue b/extralit-frontend/components/features/user-settings/UserSettingsContent.vue
index 9b3e47395..3a63099aa 100644
--- a/extralit-frontend/components/features/user-settings/UserSettingsContent.vue
+++ b/extralit-frontend/components/features/user-settings/UserSettingsContent.vue
@@ -46,6 +46,10 @@
+
+
GitHub Copilot
+
+
diff --git a/extralit-frontend/components/features/user-settings/useCopilotConnectViewModel.ts b/extralit-frontend/components/features/user-settings/useCopilotConnectViewModel.ts
new file mode 100644
index 000000000..9afa55ebb
--- /dev/null
+++ b/extralit-frontend/components/features/user-settings/useCopilotConnectViewModel.ts
@@ -0,0 +1,35 @@
+import { useFetch, onBeforeUnmount } from "@nuxtjs/composition-api";
+import { useResolve } from "ts-injecty";
+import { computed } from "vue-demi";
+import { GitHubAuthUseCase } from "~/v1/domain/usecases/github-auth-use-case";
+import { useGitHubAuth } from "~/v1/infrastructure/storage/GitHubAuthStorage";
+
+export const useCopilotConnectViewModel = () => {
+ const gitHubAuthUseCase = useResolve(GitHubAuthUseCase);
+ const store = useGitHubAuth();
+
+ const isAuthenticated = computed(() => store.state.isAuthenticated);
+ const isPending = computed(() => store.state.isPending);
+ const userCode = computed(() => store.state.userCode);
+ const verificationUri = computed(() => store.state.verificationUri);
+
+ useFetch(async () => {
+ await gitHubAuthUseCase.checkStatus();
+ });
+
+ const connectCopilot = async () => {
+ await gitHubAuthUseCase.initiateLogin();
+ };
+
+ onBeforeUnmount(() => {
+ gitHubAuthUseCase.clearPolling();
+ });
+
+ return {
+ isAuthenticated,
+ isPending,
+ userCode,
+ verificationUri,
+ connectCopilot,
+ };
+};
diff --git a/extralit-frontend/v1/di/di.ts b/extralit-frontend/v1/di/di.ts
index 6a819c978..3ed6f8e3a 100644
--- a/extralit-frontend/v1/di/di.ts
+++ b/extralit-frontend/v1/di/di.ts
@@ -25,6 +25,7 @@ import {
UserRepository,
HubRepository,
JobRepository,
+ GitHubAuthRepository,
} from "@/v1/infrastructure/repositories";
import { useLocalStorage, useRole, useRoutes } from "@/v1/infrastructure/services";
@@ -35,6 +36,7 @@ import { useDatasets } from "@/v1/infrastructure/storage/DatasetsStorage";
import { useMetrics } from "@/v1/infrastructure/storage/MetricsStorage";
import { useDatasetSetting } from "@/v1/infrastructure/storage/DatasetSettingStorage";
import { useWorkspaces } from "@/v1/infrastructure/storage/WorkspaceStorage";
+import { useGitHubAuth } from "@/v1/infrastructure/storage/GitHubAuthStorage";
import { GetHfDatasetCreationUseCase } from "~/v1/domain/usecases/get-hf-dataset-creation-use-case";
import { GetDatasetsUseCase } from "@/v1/domain/usecases/get-datasets-use-case";
@@ -81,6 +83,7 @@ import { UpdateDatasetUseCase } from "@/v1/domain/usecases/update-dataset-use-ca
import { GetFirstRecordFromHub } from "@/v1/domain/usecases/get-first-record-from-hub";
import { ExportDatasetToHubUseCase } from "@/v1/domain/usecases/export-dataset-to-hub-use-case";
import { AuthLoginUseCase } from "@/v1/domain/usecases/auth-login-use-case";
+import { GitHubAuthUseCase } from "@/v1/domain/usecases/github-auth-use-case";
import { FileParsingService } from "~/v1/domain/services/FileParsingService";
import { PdfMatchingService } from "@/v1/domain/services/FileMatchingService";
@@ -217,6 +220,9 @@ export const loadDependencyContainer = (context: Context) => {
register(ExportDatasetToHubUseCase).withDependencies(DatasetRepository, useLocalStorage).build(),
+ register(GitHubAuthRepository).withDependency(useAxios).build(),
+ register(GitHubAuthUseCase).withDependencies(GitHubAuthRepository, useGitHubAuth).build(),
+
register(FileParsingService).build(),
register(PdfMatchingService).build(),
];
diff --git a/extralit-frontend/v1/domain/usecases/github-auth-use-case.ts b/extralit-frontend/v1/domain/usecases/github-auth-use-case.ts
new file mode 100644
index 000000000..84d4450b7
--- /dev/null
+++ b/extralit-frontend/v1/domain/usecases/github-auth-use-case.ts
@@ -0,0 +1,99 @@
+import { GitHubAuthRepository } from "@/v1/infrastructure/repositories/GitHubAuthRepository";
+
+export class GitHubAuthUseCase {
+ private pollingTimer: ReturnType | null = null;
+
+ constructor(
+ private readonly repository: GitHubAuthRepository,
+ private readonly store: any
+ ) {}
+
+ async checkStatus(): Promise {
+ try {
+ const { authenticated } = await this.repository.getStatus();
+ const current = this.store.get();
+ this.store.save({
+ ...current,
+ isAuthenticated: authenticated,
+ isPending: false,
+ userCode: null,
+ verificationUri: null,
+ deviceCode: null,
+ });
+ } catch {
+ // If the check fails, leave current state unchanged
+ }
+ }
+
+ async initiateLogin(): Promise {
+ const response = await this.repository.initiateLogin();
+
+ const current = this.store.get();
+ this.store.save({
+ ...current,
+ isPending: true,
+ userCode: response.user_code,
+ verificationUri: response.verification_uri,
+ deviceCode: response.device_code,
+ isAuthenticated: false,
+ });
+
+ this.startPolling(response.device_code, response.interval);
+ }
+
+ clearPolling(): void {
+ if (this.pollingTimer) {
+ clearInterval(this.pollingTimer);
+ this.pollingTimer = null;
+ }
+ }
+
+ private startPolling(deviceCode: string, intervalSeconds: number): void {
+ this.clearPolling();
+
+ // Use at least 5 seconds between polls to avoid rate limiting
+ const pollInterval = Math.max(intervalSeconds, 5) * 1000;
+
+ this.pollingTimer = setInterval(async () => {
+ try {
+ const { status } = await this.repository.pollToken(deviceCode);
+
+ if (status === "authorized") {
+ this.clearPolling();
+ const current = this.store.get();
+ this.store.save({
+ ...current,
+ isAuthenticated: true,
+ isPending: false,
+ userCode: null,
+ verificationUri: null,
+ deviceCode: null,
+ });
+ } else if (status === "error") {
+ this.clearPolling();
+ const current = this.store.get();
+ this.store.save({
+ ...current,
+ isAuthenticated: false,
+ isPending: false,
+ userCode: null,
+ verificationUri: null,
+ deviceCode: null,
+ });
+ }
+ // "pending" β keep polling
+ } catch {
+ this.clearPolling();
+ const current = this.store.get();
+ this.store.save({
+ ...current,
+ isAuthenticated: false,
+ isPending: false,
+ userCode: null,
+ verificationUri: null,
+ deviceCode: null,
+ });
+ }
+ }, pollInterval);
+ }
+}
diff --git a/extralit-frontend/v1/infrastructure/repositories/GitHubAuthRepository.ts b/extralit-frontend/v1/infrastructure/repositories/GitHubAuthRepository.ts
new file mode 100644
index 000000000..dfa459aca
--- /dev/null
+++ b/extralit-frontend/v1/infrastructure/repositories/GitHubAuthRepository.ts
@@ -0,0 +1,46 @@
+import { type NuxtAxiosInstance } from "@nuxtjs/axios";
+
+interface AuthStatusResponse {
+ authenticated: boolean;
+ username: string;
+}
+
+interface DeviceFlowResponse {
+ device_code: string;
+ user_code: string;
+ verification_uri: string;
+ expires_in: number;
+ interval: number;
+}
+
+interface PollTokenResponse {
+ status: "pending" | "authorized" | "error";
+ message?: string;
+}
+
+export class GitHubAuthRepository {
+ // Take the standard authenticated Axios instance directly
+ constructor(private readonly axios: NuxtAxiosInstance) { }
+
+ async getStatus(): Promise {
+ const { data } = await this.axios.get(
+ "v1/auth/github/status"
+ );
+ return data;
+ }
+
+ async initiateLogin(): Promise {
+ const { data } = await this.axios.post(
+ "v1/auth/github/login"
+ );
+ return data;
+ }
+
+ async pollToken(deviceCode: string): Promise {
+ const { data } = await this.axios.post(
+ "v1/auth/github/poll",
+ { device_code: deviceCode }
+ );
+ return data;
+ }
+}
\ No newline at end of file
diff --git a/extralit-frontend/v1/infrastructure/repositories/index.ts b/extralit-frontend/v1/infrastructure/repositories/index.ts
index cb8fad438..320194c38 100644
--- a/extralit-frontend/v1/infrastructure/repositories/index.ts
+++ b/extralit-frontend/v1/infrastructure/repositories/index.ts
@@ -16,3 +16,4 @@ export * from "./UserRepository";
export * from "./VectorRepository";
export * from "./DocumentRepository";
export * from "./WorkspaceRepository";
+export * from "./GitHubAuthRepository";
diff --git a/extralit-frontend/v1/infrastructure/storage/GitHubAuthStorage.ts b/extralit-frontend/v1/infrastructure/storage/GitHubAuthStorage.ts
new file mode 100644
index 000000000..96df57794
--- /dev/null
+++ b/extralit-frontend/v1/infrastructure/storage/GitHubAuthStorage.ts
@@ -0,0 +1,15 @@
+import { useStoreFor } from "@/v1/store/create";
+
+class GitHubAuthState {
+ constructor(
+ public readonly isAuthenticated: boolean = false,
+ public readonly isPending: boolean = false,
+ public readonly userCode: string | null = null,
+ public readonly verificationUri: string | null = null,
+ public readonly deviceCode: string | null = null
+ ) {}
+}
+
+const useStoreForGitHubAuth = useStoreFor(GitHubAuthState);
+
+export const useGitHubAuth = () => useStoreForGitHubAuth();
diff --git a/extralit-server/pdm.lock b/extralit-server/pdm.lock
index 9dd229c3d..c2a0c4a5b 100644
--- a/extralit-server/pdm.lock
+++ b/extralit-server/pdm.lock
@@ -3,4344 +3,7 @@
[metadata]
groups = ["default", "marker", "postgresql", "test"]
-strategy = []
+strategy = ["inherit_metadata"]
+targets = []
lock_version = "4.5.0"
-content_hash = "sha256:c3a2035f7b8cc1ef9c8d04cc9ded68195f03418c57b861d1b5d9c60b08585a57"
-
-[[metadata.targets]]
-requires_python = ">=3.10"
-
-[[package]]
-name = "aioboto3"
-version = "15.1.0"
-summary = ""
-dependencies = [
- "aiobotocore[boto3]",
- "aiofiles",
-]
-files = [
- {file = "aioboto3-15.1.0-py3-none-any.whl", hash = "sha256:66006142a2ccc7d6d07aa260ba291c4922b6767d270ba42f95c59e85d8b3e645"},
- {file = "aioboto3-15.1.0.tar.gz", hash = "sha256:37763bbc6321ceb479106dc63bc84c8fdb59dd02540034a12941aebef2057c5c"},
-]
-
-[[package]]
-name = "aiobotocore"
-version = "2.24.0"
-summary = ""
-dependencies = [
- "aiohttp",
- "aioitertools",
- "botocore",
- "jmespath",
- "multidict",
- "python-dateutil",
- "wrapt",
-]
-files = [
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- {file = "aiobotocore-2.24.0.tar.gz", hash = "sha256:b32c0c45d38c22a18ce395a0b5448606c5260603296a152895b5bdb40ab3139d"},
-]
-
-[[package]]
-name = "aiobotocore"
-version = "2.24.0"
-extras = ["boto3"]
-summary = ""
-dependencies = [
- "aiobotocore==2.24.0",
- "boto3",
-]
-files = [
- {file = "aiobotocore-2.24.0-py3-none-any.whl", hash = "sha256:72bb1f8eb1b962779a95e1bcc9cf35bc33196ad763b622a40ae7fa9d2e95c87c"},
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-]
-
-[[package]]
-name = "aiofiles"
-version = "24.1.0"
-summary = ""
-files = [
- {file = "aiofiles-24.1.0-py3-none-any.whl", hash = "sha256:b4ec55f4195e3eb5d7abd1bf7e061763e864dd4954231fb8539a0ef8bb8260e5"},
- {file = "aiofiles-24.1.0.tar.gz", hash = "sha256:22a075c9e5a3810f0c2e48f3008c94d68c65d763b9b03857924c99e57355166c"},
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-
-[[package]]
-name = "aiohappyeyeballs"
-version = "2.4.3"
-summary = ""
-files = [
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-]
-
-[[package]]
-name = "aiohttp"
-version = "3.10.10"
-summary = ""
-dependencies = [
- "aiohappyeyeballs",
- "aiosignal",
- "async-timeout; python_full_version < \"3.11\"",
- "attrs",
- "frozenlist",
- "multidict",
- "yarl",
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diff --git a/extralit-server/pyproject.toml b/extralit-server/pyproject.toml
index 767c557d1..5ceea5f0d 100644
--- a/extralit-server/pyproject.toml
+++ b/extralit-server/pyproject.toml
@@ -3,7 +3,8 @@ name = "extralit-server"
dynamic = ["version"]
description = "Open-source tool for accurate & fast scientific literature data extraction with LLM and human-in-the-loop."
readme = "README.md"
-requires-python = ">=3.10"
+# requires-python = ">=3.11"
+requires-python = ">=3.11,<3.14"
license = { text = "Apache-2.0" }
keywords = [
"literature-review",
@@ -13,12 +14,8 @@ keywords = [
"human-in-the-loop",
"mlops",
]
-authors = [
- { name = "Extralit Labs", email = "extralit.contact@gmail.com" },
-]
-maintainers = [
- { name = "Extralit Labs", email = "extralit.contact@gmail.com" },
-]
+authors = [{ name = "Extralit Labs", email = "extralit.contact@gmail.com" }]
+maintainers = [{ name = "Extralit Labs", email = "extralit.contact@gmail.com" }]
dependencies = [
# Basic dependencies
"fastapi ~= 0.115.0",
@@ -47,6 +44,8 @@ dependencies = [
"httpx ~= 0.27.0",
"oauthlib ~= 3.2.0",
"social-auth-core ~= 4.5.0",
+ # LiteLLM for chat integration
+ "litellm >= 1.60.0",
# Background processing
"rq~=2.4.1",
"lazy-loader>=0.4",
@@ -55,8 +54,8 @@ dependencies = [
# For logging, tracebacks, printing, progressbars
"rich != 13.1.0",
# For CLI
- "typer>=0.19.1", # spaCy only supports typer<0.10.0
- "click >= 8.2.0", # click >=8.2.0 has TypeError: Parameter.make_metavar() missing 1 required positional argument: 'ctx'
+ "typer>=0.19.1", # spaCy only supports typer<0.10.0
+ "click >= 8.2.0", # click >=8.2.0 has TypeError: Parameter.make_metavar() missing 1 required positional argument: 'ctx'
"packaging>=23.2",
# For Webhooks
"standardwebhooks>=1.0.0",
@@ -75,6 +74,8 @@ dependencies = [
"ocrmypdf>=16.11.0",
"pdf2image>=1.17.0",
"opencv-python-headless>=4.11.0.86",
+ # Local extralit package for OCR jobs
+ "extralit @ file:///${PROJECT_ROOT}/../extralit",
]
[project.optional-dependencies]
@@ -121,7 +122,7 @@ test = [
"pytest-randomly>=3.16.0",
# For mocking httpx requests and responses
"respx>=0.21.1",
- "ruff>=0.12.11"
+ "ruff>=0.12.11",
]
[tool.pytest.ini_options]
@@ -174,15 +175,15 @@ target-version = "py310"
[tool.ruff.lint]
select = [
- "F", # Pyflakes (undefined names, logical issues)
- "E7", # Syntax/indentation errors
- "E9", # Runtime-like errors
- "E4", # Import-related errors (E401, E402, etc.)
- "B012", # return in finally (can suppress real exceptions)
- "B", # flake8-bugbear (broader than just B012)
- "C4", # flake8-comprehensions
- "I", # isort (import sorting)
- "UP", # pyupgrade (modern Python syntax)
+ "F", # Pyflakes (undefined names, logical issues)
+ "E7", # Syntax/indentation errors
+ "E9", # Runtime-like errors
+ "E4", # Import-related errors (E401, E402, etc.)
+ "B012", # return in finally (can suppress real exceptions)
+ "B", # flake8-bugbear (broader than just B012)
+ "C4", # flake8-comprehensions
+ "I", # isort (import sorting)
+ "UP", # pyupgrade (modern Python syntax)
"ASYNC", # flake8-async - async/await specific rules
"PLE", # pylint errors (includes await-outside-async)
"FAST", # FastAPI-specific rules (valuable for your backend)
@@ -190,23 +191,33 @@ select = [
]
ignore = [
- "E402", # imports not at top (lazy / optional import patterns)
- "B904", # exception chaining (will phase in later)
- "UP007", # | union syntax modernization
- "UP045", # Optional[...] -> X | None modernization
+ "E402", # imports not at top (lazy / optional import patterns)
+ "B904", # exception chaining (will phase in later)
+ "UP007", # | union syntax modernization
+ "UP045", # Optional[...] -> X | None modernization
"UP038",
- "B027", # empty abstract method not marked abstract
- "B024", # abstract base class without abstract methods
- "B017", # broad exception asserts in tests
- "RUF012", # mutable class var typing inference
- "B008", # FastAPI Depends pattern
+ "B027", # empty abstract method not marked abstract
+ "B024", # abstract base class without abstract methods
+ "B017", # broad exception asserts in tests
+ "RUF012", # mutable class var typing inference
+ "B008", # FastAPI Depends pattern
"FAST002", # FastAPI Depends suggestion
]
[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["F401", "F403", "I001"] # Ignore unused imports and wildcard imports in __init__.py
-"tests/**/*.py" = ["ASYNC", "F821"] # More lenient async rules in tests (ignore undefined names like forward refs/fixtures)
-"src/extralit_server/cli/**/*.py" = ["UP007", "UP045"] # Typer doesn't support new union syntax
+"__init__.py" = [
+ "F401",
+ "F403",
+ "I001",
+] # Ignore unused imports and wildcard imports in __init__.py
+"tests/**/*.py" = [
+ "ASYNC",
+ "F821",
+] # More lenient async rules in tests (ignore undefined names like forward refs/fixtures)
+"src/extralit_server/cli/**/*.py" = [
+ "UP007",
+ "UP045",
+] # Typer doesn't support new union syntax
[tool.pdm.scripts]
_.env_file = ".env.dev"
diff --git a/extralit-server/src/extralit_server/api/handlers/v1/chat.py b/extralit-server/src/extralit_server/api/handlers/v1/chat.py
new file mode 100644
index 000000000..644e5f94b
--- /dev/null
+++ b/extralit-server/src/extralit_server/api/handlers/v1/chat.py
@@ -0,0 +1,339 @@
+# Copyright 2024-present, Extralit Labs, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+"""
+Chat endpoint using LiteLLM with GitHub Copilot and RAG support.
+"""
+
+import logging
+from typing import Annotated, Any
+from uuid import UUID
+
+import litellm
+from fastapi import APIRouter, Depends, HTTPException
+from pydantic import BaseModel, Field
+from sqlalchemy.ext.asyncio import AsyncSession
+from starlette.responses import StreamingResponse
+
+from extralit_server.contexts import datasets as dataset_ctx
+from extralit_server.database import get_async_db
+from extralit_server.models import Dataset, User, VectorSettings
+from extralit_server.search_engine import SearchEngine, get_search_engine
+from extralit_server.security import auth
+from extralit_server.utils.auth_helpers import GitHubDeviceFlowAuth
+from extralit_server.utils.litellm_context import LiteLLMContext
+
+_LOGGER = logging.getLogger(__name__)
+
+router = APIRouter(tags=["chat"])
+
+
+class ChatMessage(BaseModel):
+ """A single chat message."""
+
+ role: str = Field(..., description="Role of the message sender (user, assistant, system)")
+ content: str = Field(..., description="Content of the message")
+
+
+class ChatRequest(BaseModel):
+ """Request model for chat endpoint."""
+
+ model: str = Field(default="copilot", description="Model to use for chat (e.g., 'copilot')")
+ messages: list[ChatMessage] = Field(..., description="List of chat messages")
+ stream: bool = Field(default=True, description="Whether to stream the response")
+ dataset_id: UUID | None = Field(default=None, description="Optional dataset ID for RAG retrieval")
+ top_k: int = Field(default=5, ge=1, le=20, description="Number of documents to retrieve for RAG")
+
+
+# VS Code headers to mimic for GitHub Copilot compatibility
+COPILOT_HEADERS = {
+ "Editor-Version": "vscode/1.96.2",
+ "Editor-Plugin-Version": "copilot/1.256.0",
+ "User-Agent": "GithubCopilot/1.256.0",
+ "Copilot-Integration-Id": "vscode-chat",
+}
+
+
+def resolve_model_string(model: str) -> str:
+ """
+ Resolve user-friendly model names to LiteLLM model strings.
+
+ Args:
+ model: User-provided model name (e.g., "copilot", "gpt-4")
+
+ Returns:
+ LiteLLM-compatible model string
+ """
+
+ model_mapping = {
+ "copilot": "gpt-4o", # Updated to gpt-4o which is supported
+ "github-copilot": "gpt-4o",
+ }
+
+ # If it's not in the map, use it as is, but strip github/ if present
+ # to avoid duplication when we pass the provider explicitly
+ resolved = model_mapping.get(model.lower(), model)
+ return resolved.replace("github/", "")
+
+
+async def retrieve_context(
+ db: AsyncSession,
+ search_engine: SearchEngine,
+ dataset_id: UUID,
+ query_text: str,
+ github_token: str,
+ top_k: int = 5,
+) -> str | None:
+ """
+ Retrieve relevant context from a dataset using RAG.
+
+ Args:
+ db: Database session
+ search_engine: Search engine instance
+ dataset_id: ID of the dataset to search
+ query_text: User's query text
+ github_token: GitHub token for embedding API
+ top_k: Number of results to retrieve
+
+ Returns:
+ Formatted context string or None if retrieval fails
+ """
+ try:
+ # Fetch the dataset
+ dataset = await Dataset.get_by(db, id=dataset_id)
+ if not dataset:
+ _LOGGER.warning(f"Dataset {dataset_id} not found")
+ return None
+
+ # Get vector settings for this dataset (use first available or "default")
+ vector_settings = await VectorSettings.get_by(db, dataset_id=dataset.id)
+ if not vector_settings:
+ _LOGGER.warning(f"No vector settings found for dataset {dataset_id}")
+ return None
+
+ _LOGGER.info(f"Generating embedding for query: {query_text[:50]}...")
+
+ # Inject token directly β no os.environ mutation (async-safe)
+ embedding_response = await litellm.aembedding(
+ model="text-embedding-3-small",
+ input=query_text,
+ custom_llm_provider="github",
+ api_key=github_token,
+ )
+ query_embedding = embedding_response["data"][0]["embedding"]
+
+ _LOGGER.info(f"Generated embedding with {len(query_embedding)} dimensions")
+
+ # Perform similarity search
+ search_results = await search_engine.similarity_search(
+ dataset=dataset,
+ vector_settings=vector_settings,
+ value=query_embedding,
+ max_results=top_k,
+ threshold=0.6, # Minimum similarity threshold
+ )
+
+ if not search_results.items:
+ _LOGGER.info("No relevant documents found")
+ return None
+
+ _LOGGER.info(f"Found {len(search_results.items)} relevant documents")
+
+ # Fetch the actual record data
+ record_ids = [item.record_id for item in search_results.items]
+ records = await dataset_ctx.get_records_by_ids(
+ db=db,
+ dataset_id=dataset.id,
+ records_ids=record_ids,
+ )
+
+ # Build context from retrieved records
+ context_chunks = []
+ for record in records:
+ # Extract text from record fields
+ if record.fields:
+ for field_name, field_value in record.fields.items():
+ if isinstance(field_value, str):
+ context_chunks.append(f"[{field_name}]: {field_value}")
+ elif isinstance(field_value, list):
+ # Handle chat fields (list of messages)
+ for msg in field_value:
+ if isinstance(msg, dict) and "content" in msg:
+ context_chunks.append(f"[{field_name}]: {msg['content']}")
+
+ if not context_chunks:
+ _LOGGER.warning("No text content found in retrieved records")
+ return None
+
+ context = "\n\n".join(context_chunks[: top_k * 3]) # Limit total context
+ _LOGGER.info(f"Built context with {len(context)} characters from {len(context_chunks)} chunks")
+
+ return context
+
+ except Exception as e:
+ _LOGGER.error(f"Error during RAG retrieval: {e}", exc_info=True)
+ return None
+
+
+@router.post("/chat")
+async def chat(
+ request: ChatRequest,
+ db: Annotated[AsyncSession, Depends(get_async_db)],
+ search_engine: Annotated[SearchEngine, Depends(get_search_engine)],
+ current_user: User = Depends(auth.get_current_user),
+) -> StreamingResponse:
+ """
+ Chat endpoint using LiteLLM with GitHub Copilot and optional RAG.
+
+ This endpoint requires the user to be authenticated with both Extralit
+ and GitHub (via the /auth/github/login flow).
+
+ If dataset_id is provided, the endpoint will perform RAG retrieval:
+ 1. Generate embedding for the user's query
+ 2. Search for relevant documents in the dataset
+ 3. Inject retrieved context into the system prompt
+
+ Args:
+ request: Chat request with model, messages, and optional dataset_id
+ current_user: Authenticated Extralit user
+ db: Database session (injected for RAG)
+ search_engine: Search engine instance (injected for RAG)
+
+ Returns:
+ StreamingResponse with chat completion
+
+ Raises:
+ HTTPException: If user is not authenticated with GitHub
+ """
+ # Check if user has GitHub token
+ github_auth = GitHubDeviceFlowAuth(username=current_user.username)
+ if not github_auth.is_authenticated():
+ raise HTTPException(
+ status_code=401,
+ detail="Not authenticated with GitHub. Please call /auth/github/login first.",
+ )
+
+ # Load the token to set in environment
+ token_data = github_auth.load_token()
+ if not token_data or "access_token" not in token_data:
+ raise HTTPException(
+ status_code=401,
+ detail="Invalid GitHub token. Please re-authenticate.",
+ )
+
+ # Resolve model string
+ litellm_model = resolve_model_string(request.model)
+
+ _LOGGER.info(
+ f"Chat request from {current_user.username} using model {litellm_model}"
+ + (f" with RAG (dataset_id={request.dataset_id})" if request.dataset_id else "")
+ )
+
+ # Convert messages to LiteLLM format
+ messages = [{"role": msg.role, "content": msg.content} for msg in request.messages]
+
+ # RAG: Retrieve context if dataset_id is provided
+ context = None
+ if request.dataset_id:
+ # Extract user's last message as query
+ user_messages = [msg for msg in messages if msg["role"] == "user"]
+ if user_messages:
+ query_text = user_messages[-1]["content"]
+ context = await retrieve_context(
+ db=db,
+ search_engine=search_engine,
+ dataset_id=request.dataset_id,
+ query_text=query_text,
+ github_token=token_data["access_token"],
+ top_k=request.top_k,
+ )
+
+ # Inject context into messages if available
+ if context:
+ system_message = {
+ "role": "system",
+ "content": (
+ "You are a helpful assistant. Use the following context from the knowledge base "
+ "to answer the user's question. If the context doesn't contain relevant information, "
+ "you can use your general knowledge but mention that the information isn't in the context.\n\n"
+ f"Context:\n{context}"
+ ),
+ }
+ # Insert system message at the beginning
+ messages = [system_message, *messages]
+ _LOGGER.info(f"Injected RAG context ({len(context)} chars) into conversation")
+
+ async def stream_response():
+ """Stream the chat completion response."""
+ try:
+ # LiteLLMContext handles XDG_CONFIG_HOME isolation (not token injection)
+ with LiteLLMContext(username=current_user.username):
+ # Inject token explicitly β no os.environ mutation (async-safe)
+ response = await litellm.acompletion(
+ model=litellm_model,
+ messages=messages,
+ stream=request.stream,
+ extra_headers=COPILOT_HEADERS,
+ custom_llm_provider="github",
+ api_key=token_data["access_token"],
+ )
+
+ if request.stream:
+ # Stream the response chunks
+ async for chunk in response:
+ if chunk.choices and len(chunk.choices) > 0:
+ delta = chunk.choices[0].delta
+ if hasattr(delta, "content") and delta.content:
+ # Send as SSE format (Standard Extralit/ChatGPT format)
+ yield f"data: {delta.content}\n\n"
+ yield "data: [DONE]\n\n"
+ else:
+ # Non-streaming response
+ if response.choices and len(response.choices) > 0:
+ content = response.choices[0].message.content
+ yield f"data: {content}\n\n"
+ yield "data: [DONE]\n\n"
+
+ except Exception as e:
+ _LOGGER.error(f"Error in chat completion for {current_user.username}: {e}")
+ # Ensure the error is returned in a format the frontend can handle
+ error_msg = str(e).replace('"', '\\"')
+ yield f'data: {{"error": "{error_msg}"}}\n\n'
+
+ return StreamingResponse(
+ stream_response(),
+ media_type="text/event-stream",
+ )
+
+
+@router.get("/chat/models")
+async def list_models(current_user: User = Depends(auth.get_current_user)) -> dict[str, Any]:
+ """
+ List available chat models.
+
+ Returns:
+ Dictionary with available models
+ """
+ return {
+ "models": [
+ {
+ "id": "copilot",
+ "name": "GitHub Copilot",
+ "description": "GitHub Copilot chat model with optional RAG support",
+ "requires_auth": True,
+ "supports_rag": True,
+ },
+ ],
+ }
diff --git a/extralit-server/src/extralit_server/api/handlers/v1/github_auth.py b/extralit-server/src/extralit_server/api/handlers/v1/github_auth.py
new file mode 100644
index 000000000..ea0f1a066
--- /dev/null
+++ b/extralit-server/src/extralit_server/api/handlers/v1/github_auth.py
@@ -0,0 +1,181 @@
+# Copyright 2024-present, Extralit Labs, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+GitHub authentication endpoints for Copilot integration.
+"""
+
+import logging
+
+from fastapi import APIRouter, Depends
+from pydantic import BaseModel
+
+from extralit_server.models import User
+from extralit_server.security import auth
+from extralit_server.utils.auth_helpers import GitHubDeviceFlowAuth
+
+_LOGGER = logging.getLogger(__name__)
+
+router = APIRouter(tags=["auth"])
+
+
+class AuthStatusResponse(BaseModel):
+ """Response model for auth status check."""
+
+ authenticated: bool
+ username: str
+
+
+class DeviceFlowResponse(BaseModel):
+ """Response model for device flow initiation."""
+
+ device_code: str # <--- ADDED THIS FIELD
+ user_code: str
+ verification_uri: str
+ expires_in: int
+ interval: int
+
+
+@router.get("/auth/github/status")
+async def get_auth_status(current_user: User = Depends(auth.get_current_user)) -> AuthStatusResponse:
+ """
+ Check if the current user has authenticated with GitHub for Copilot access.
+
+ Returns:
+ AuthStatusResponse with authentication status and username
+ """
+ github_auth = GitHubDeviceFlowAuth(username=current_user.username)
+ is_authenticated = github_auth.is_authenticated()
+
+ _LOGGER.info(f"Auth status check for {current_user.username}: {is_authenticated}")
+
+ return AuthStatusResponse(
+ authenticated=is_authenticated,
+ username=current_user.username,
+ )
+
+
+@router.post("/auth/github/login")
+async def initiate_github_login(current_user: User = Depends(auth.get_current_user)) -> DeviceFlowResponse:
+ """
+ Initiate GitHub Device Flow authentication.
+
+ This endpoint starts the OAuth Device Flow and returns the user code
+ and verification URI that the user should visit to authorize the application.
+
+ Returns:
+ DeviceFlowResponse with device_code, user_code, verification_uri, expires_in, and interval
+
+ Raises:
+ ValueError: If GitHub client ID is not configured
+ """
+ github_auth = GitHubDeviceFlowAuth(username=current_user.username)
+
+ try:
+ flow_data = await github_auth.initiate_flow()
+ _LOGGER.info(f"Initiated GitHub Device Flow for {current_user.username}")
+
+ # Return device_code so the client can use it to poll for the token
+ return DeviceFlowResponse(
+ device_code=flow_data["device_code"], # <--- ADDED THIS ASSIGNMENT
+ user_code=flow_data["user_code"],
+ verification_uri=flow_data["verification_uri"],
+ expires_in=flow_data["expires_in"],
+ interval=flow_data["interval"],
+ )
+ except ValueError as e:
+ _LOGGER.error(f"Failed to initiate GitHub Device Flow: {e}")
+ raise
+
+
+class PollTokenRequest(BaseModel):
+ """Request model for polling token."""
+
+ device_code: str
+
+
+class PollTokenResponse(BaseModel):
+ """Response model for polling token."""
+
+ status: str # "pending", "authorized", "error"
+ message: str | None = None
+
+
+@router.post("/auth/github/poll")
+async def poll_github_token(
+ request: PollTokenRequest,
+ current_user: User = Depends(auth.get_current_user),
+) -> PollTokenResponse:
+ """
+ Poll for GitHub access token after user authorization.
+
+ This endpoint should be called by the client after the user has visited
+ the verification URI and entered their code.
+
+ Args:
+ request: Contains the device_code from the login initiation
+
+ Returns:
+ PollTokenResponse indicating status of authorization
+
+ Raises:
+ ValueError: If authorization fails or expires
+ """
+ github_auth = GitHubDeviceFlowAuth(username=current_user.username)
+
+ try:
+ # Poll with a short timeout (single attempt)
+ token_data = await github_auth.poll_for_token(
+ device_code=request.device_code,
+ interval=5,
+ timeout=10, # Just one quick check
+ )
+
+ # Save the token
+ github_auth.save_token(token_data)
+
+ _LOGGER.info(f"Successfully authorized and saved token for {current_user.username}")
+
+ return PollTokenResponse(
+ status="authorized",
+ message="Successfully authenticated with GitHub",
+ )
+ except TimeoutError:
+ # User hasn't authorized yet
+ return PollTokenResponse(
+ status="pending",
+ message="Authorization pending",
+ )
+ except ValueError as e:
+ _LOGGER.error(f"Token polling error for {current_user.username}: {e}")
+ return PollTokenResponse(
+ status="error",
+ message=str(e),
+ )
+
+
+@router.delete("/auth/github/logout")
+async def logout_github(current_user: User = Depends(auth.get_current_user)) -> dict[str, str]:
+ """
+ Clear the stored GitHub token for the current user.
+
+ Returns:
+ Success message
+ """
+ github_auth = GitHubDeviceFlowAuth(username=current_user.username)
+ github_auth.clear_token()
+
+ _LOGGER.info(f"Logged out GitHub for {current_user.username}")
+
+ return {"message": "Successfully logged out from GitHub"}
diff --git a/extralit-server/src/extralit_server/api/routes.py b/extralit-server/src/extralit_server/api/routes.py
index 20ce8322f..b483da913 100644
--- a/extralit-server/src/extralit_server/api/routes.py
+++ b/extralit-server/src/extralit_server/api/routes.py
@@ -22,6 +22,9 @@
from extralit_server._version import __version__ as extralit_version
from extralit_server.api.errors.v1.exception_handlers import add_exception_handlers as add_exception_handlers_v1
from extralit_server.api.handlers.v1 import authentication as authentication_v1
+from extralit_server.api.handlers.v1 import (
+ chat as chat_v1,
+)
from extralit_server.api.handlers.v1 import (
datasets as datasets_v1,
)
@@ -34,6 +37,9 @@
from extralit_server.api.handlers.v1 import (
files as files_v1,
)
+from extralit_server.api.handlers.v1 import (
+ github_auth as github_auth_v1,
+)
from extralit_server.api.handlers.v1 import (
imports as imports_v1,
)
@@ -117,6 +123,8 @@ def create_api_v1():
files_v1.router,
models_v1.router,
imports_v1.router,
+ github_auth_v1.router,
+ chat_v1.router,
]:
api_v1.include_router(router)
diff --git a/extralit-server/src/extralit_server/jobs/preload.py b/extralit-server/src/extralit_server/jobs/preload.py
index 76ef65204..336950a27 100644
--- a/extralit-server/src/extralit_server/jobs/preload.py
+++ b/extralit-server/src/extralit_server/jobs/preload.py
@@ -31,7 +31,7 @@
document_jobs,
hub_jobs,
import_jobs,
- # ocr_jobs,
+ ocr_jobs,
webhook_jobs,
)
from extralit_server.models.database import Dataset, Document, Record, User, Workspace # noqa: F401
diff --git a/extralit-server/src/extralit_server/utils/auth_helpers.py b/extralit-server/src/extralit_server/utils/auth_helpers.py
new file mode 100644
index 000000000..f175ee0ec
--- /dev/null
+++ b/extralit-server/src/extralit_server/utils/auth_helpers.py
@@ -0,0 +1,219 @@
+# Copyright 2024-present, Extralit Labs, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+GitHub Device Flow authentication utilities for GitHub Copilot integration.
+"""
+
+import asyncio
+import json
+import logging
+import time
+from pathlib import Path
+from typing import Any
+
+import httpx
+
+from extralit_server.settings import settings
+
+_LOGGER = logging.getLogger(__name__)
+
+
+class GitHubDeviceFlowAuth:
+ """
+ Helper class for GitHub Device Flow authentication.
+
+ This implements the OAuth Device Flow for authenticating with GitHub
+ to obtain tokens for GitHub Copilot access.
+
+ Uses the official VS Code OAuth app credentials to ensure compatibility
+ with GitHub Copilot.
+ """
+
+ # Official VS Code OAuth App Client ID (public, safe to hardcode)
+ # This is the ONLY client ID that GitHub Copilot accepts
+ VSCODE_CLIENT_ID = "01ab8ac9400c4e429b23"
+
+ DEVICE_CODE_URL = "https://github.com/login/device/code"
+ ACCESS_TOKEN_URL = "https://github.com/login/oauth/access_token"
+
+ # Scopes required for GitHub Copilot access
+ SCOPE = "read:user copilot"
+
+ def __init__(self, username: str):
+ """
+ Initialize the GitHub Device Flow helper.
+
+ Args:
+ username: The Extralit username (used for token storage path)
+ """
+ self.username = username
+
+ def _get_config_dir(self) -> Path:
+ """Get the user-specific config directory for token storage."""
+ config_path = Path(settings.home_path) / "data" / "users" / self.username / "config"
+ config_path.mkdir(parents=True, exist_ok=True)
+ return config_path
+
+ def _get_token_path(self) -> Path:
+ """Get the full path to the token file."""
+ return self._get_config_dir() / "github_token.json"
+
+ async def initiate_flow(self) -> dict[str, Any]:
+ """
+ Initiate the GitHub Device Flow.
+
+ Returns:
+ dict containing:
+ - device_code: Code for polling
+ - user_code: Code for user to enter
+ - verification_uri: URL for user to visit
+ - expires_in: Seconds until codes expire
+ - interval: Recommended polling interval in seconds
+
+ Raises:
+ httpx.HTTPError: If the request to GitHub fails
+ """
+ async with httpx.AsyncClient() as client:
+ response = await client.post(
+ self.DEVICE_CODE_URL,
+ data={
+ "client_id": self.VSCODE_CLIENT_ID,
+ "scope": self.SCOPE,
+ },
+ headers={"Accept": "application/json"},
+ )
+ response.raise_for_status()
+ data = response.json()
+
+ _LOGGER.info(f"Initiated GitHub Device Flow for user {self.username}")
+ return {
+ "device_code": data["device_code"],
+ "user_code": data["user_code"],
+ "verification_uri": data["verification_uri"],
+ "expires_in": data["expires_in"],
+ "interval": data["interval"],
+ }
+
+ async def poll_for_token(self, device_code: str, interval: int = 5, timeout: int = 900) -> dict[str, str]:
+ """
+ Poll GitHub for the access token after user authorization.
+
+ Args:
+ device_code: The device code from initiate_flow()
+ interval: Seconds to wait between polling attempts
+ timeout: Maximum seconds to wait for authorization
+
+ Returns:
+ dict containing:
+ - access_token: The GitHub access token
+ - token_type: Type of token (usually "bearer")
+ - scope: Granted scopes
+
+ Raises:
+ TimeoutError: If user doesn't authorize within timeout
+ ValueError: If authorization is denied or expires
+ httpx.HTTPError: If the request to GitHub fails
+ """
+ start_time = time.time()
+ async with httpx.AsyncClient() as client:
+ while True:
+ if time.time() - start_time > timeout:
+ raise TimeoutError("GitHub Device Flow timed out waiting for user authorization")
+
+ response = await client.post(
+ self.ACCESS_TOKEN_URL,
+ data={
+ "client_id": self.VSCODE_CLIENT_ID,
+ "device_code": device_code,
+ "grant_type": "urn:ietf:params:oauth:grant-type:device_code",
+ },
+ headers={"Accept": "application/json"},
+ )
+
+ data = response.json()
+
+ if "access_token" in data:
+ _LOGGER.info(f"Successfully obtained GitHub token for user {self.username}")
+ return {
+ "access_token": data["access_token"],
+ "token_type": data.get("token_type", "bearer"),
+ "scope": data.get("scope", ""),
+ }
+ elif data.get("error") == "authorization_pending":
+ # User hasn't authorized yet, keep polling
+ await asyncio.sleep(interval)
+ elif data.get("error") == "slow_down":
+ # We're polling too fast, increase interval
+ interval += 5
+ await asyncio.sleep(interval)
+ elif data.get("error") in ("expired_token", "access_denied"):
+ raise ValueError(f"GitHub authorization {data['error']}: {data.get('error_description', '')}")
+ else:
+ raise ValueError(f"Unexpected error from GitHub: {data}")
+
+ def save_token(self, token_data: dict[str, str]) -> None:
+ """
+ Save the GitHub token to disk.
+
+ Args:
+ token_data: Token data containing access_token, token_type, scope
+ """
+ token_path = self._get_token_path()
+ with open(token_path, "w") as f:
+ json.dump(token_data, f)
+
+ # Set restrictive permissions (read/write for owner only)
+ token_path.chmod(0o600)
+
+ _LOGGER.info(f"Saved GitHub token for user {self.username} to {token_path}")
+
+ def load_token(self) -> dict[str, str] | None:
+ """
+ Load the GitHub token from disk.
+
+ Returns:
+ Token data dict if exists, None otherwise
+ """
+ token_path = self._get_token_path()
+ if not token_path.exists():
+ return None
+
+ try:
+ with open(token_path) as f:
+ token_data = json.load(f)
+ _LOGGER.debug(f"Loaded GitHub token for user {self.username}")
+ return token_data
+ except (json.JSONDecodeError, OSError) as e:
+ _LOGGER.error(f"Failed to load token for user {self.username}: {e}")
+ return None
+
+ def is_authenticated(self) -> bool:
+ """
+ Check if a valid GitHub token exists for this user.
+
+ Returns:
+ True if token file exists and is readable, False otherwise
+ """
+ token_data = self.load_token()
+ return token_data is not None and "access_token" in token_data
+
+ def clear_token(self) -> None:
+ """
+ Remove the stored GitHub token.
+ """
+ token_path = self._get_token_path()
+ if token_path.exists():
+ token_path.unlink()
+ _LOGGER.info(f"Cleared GitHub token for user {self.username}")
diff --git a/extralit-server/src/extralit_server/utils/litellm_context.py b/extralit-server/src/extralit_server/utils/litellm_context.py
new file mode 100644
index 000000000..eadcc8991
--- /dev/null
+++ b/extralit-server/src/extralit_server/utils/litellm_context.py
@@ -0,0 +1,78 @@
+# Copyright 2024-present, Extralit Labs, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+Context manager for LiteLLM environment isolation.
+
+This ensures that each user's GitHub Copilot tokens are isolated
+by temporarily setting XDG_CONFIG_HOME to user-specific directories.
+"""
+
+import os
+from pathlib import Path
+from typing import Any
+
+from extralit_server.settings import settings
+
+
+class LiteLLMContext:
+ """
+ Context manager for isolating LiteLLM environment per user.
+
+ This temporarily sets XDG_CONFIG_HOME to point to a user-specific
+ directory, ensuring that LiteLLM uses the correct GitHub token
+ for each user without leakage.
+
+ Example:
+ with LiteLLMContext(username="alice"):
+ # LiteLLM will use alice's GitHub token
+ response = await litellm.acompletion(...)
+ """
+
+ def __init__(self, username: str):
+ """
+ Initialize the context manager.
+
+ Args:
+ username: The Extralit username for token isolation
+ """
+ self.username = username
+ self.user_config_dir = str(Path(settings.home_path) / "data" / "users" / username / "config")
+ self.original_xdg_config_home: str | None = None
+
+ def __enter__(self) -> "LiteLLMContext":
+ """
+ Enter the context: set XDG_CONFIG_HOME to user-specific directory.
+ """
+ # Save original value
+ self.original_xdg_config_home = os.environ.get("XDG_CONFIG_HOME")
+
+ # Set to user-specific directory
+ os.environ["XDG_CONFIG_HOME"] = self.user_config_dir
+
+ # Ensure directory exists
+ Path(self.user_config_dir).mkdir(parents=True, exist_ok=True)
+
+ return self
+
+ def __exit__(self, exc_type: Any, exc_val: Any, exc_tb: Any) -> None:
+ """
+ Exit the context: restore original XDG_CONFIG_HOME.
+ """
+ # Restore original value
+ if self.original_xdg_config_home is not None:
+ os.environ["XDG_CONFIG_HOME"] = self.original_xdg_config_home
+ else:
+ # Remove if it wasn't set before
+ os.environ.pop("XDG_CONFIG_HOME", None)
diff --git a/extralit/pyproject.toml b/extralit/pyproject.toml
index a63f5b099..4a03735dc 100644
--- a/extralit/pyproject.toml
+++ b/extralit/pyproject.toml
@@ -1,13 +1,10 @@
[project]
name = "extralit"
description = "Open-source tool for accurate & fast scientific literature data extraction with LLM and human-in-the-loop."
-authors = [
- { name = "Extralit Labs", email = "extralit.contact@gmail.com" },
-]
-maintainers = [
- { name = "Extralit Labs", email = "extralit.contact@gmail.com" },
-]
-requires-python = ">=3.9.2, <3.14"
+authors = [{ name = "Extralit Labs", email = "extralit.contact@gmail.com" }]
+maintainers = [{ name = "Extralit Labs", email = "extralit.contact@gmail.com" }]
+# requires-python = ">=3.9.2, <3.14"
+requires-python = ">=3.11,<3.14"
readme = "README.md"
license = { text = "Apache 2.0" }
@@ -19,7 +16,7 @@ dependencies = [
"huggingface_hub>=0.22.0",
"tqdm>=4.60.0",
"rich>=10.0.0",
- "datasets~=3.6.0",
+ "datasets~=3.0.2",
"pillow>=9.5.0",
"standardwebhooks>=1.0.0",
"typer>=0.9.0",
@@ -29,12 +26,9 @@ dependencies = [
"pandera[io]>=0.26.1, < 0.27.0",
"pandas>=2.3.2",
- "llama-index-embeddings-openai>=0.5.0"
-]
-nlp = [
- "textdescriptives",
- "setfit ~= 0.7.0",
+ "llama-index-embeddings-openai>=0.5.0",
]
+nlp = ["textdescriptives", "setfit ~= 0.7.0"]
[build-system]
requires = ["pdm-backend>=2.0.0", "setuptools>=68.0.0"]
@@ -45,15 +39,15 @@ line-length = 120
[tool.ruff.lint]
select = [
- "F", # Pyflakes (undefined names, logical issues)
- "E7", # Syntax/indentation errors
- "E9", # Runtime-like errors
- "E4", # Import-related errors (E401, E402, etc.)
- "B012", # return in finally (can suppress real exceptions)
- "B", # flake8-bugbear (broader than just B012)
- "C4", # flake8-comprehensions
- "I", # isort (import sorting)
- "UP", # pyupgrade (modern Python syntax)
+ "F", # Pyflakes (undefined names, logical issues)
+ "E7", # Syntax/indentation errors
+ "E9", # Runtime-like errors
+ "E4", # Import-related errors (E401, E402, etc.)
+ "B012", # return in finally (can suppress real exceptions)
+ "B", # flake8-bugbear (broader than just B012)
+ "C4", # flake8-comprehensions
+ "I", # isort (import sorting)
+ "UP", # pyupgrade (modern Python syntax)
"ASYNC", # flake8-async - async/await specific rules
"PLE", # pylint errors (includes await-outside-async)
"FAST", # FastAPI-specific rules (valuable for your backend)
@@ -70,7 +64,7 @@ ignore = [
"RUF012",
"B008",
"FAST002",
- "B023"
+ "B023",
]
[tool.ruff.lint.per-file-ignores]