krassowski · krassowski · Jun 19, 2022
diff --git a/.eslintrc.js b/.eslintrc.js
@@ -33,7 +33,7 @@ module.exports = {
       { avoidEscape: true, allowTemplateLiterals: false }
     ],
     curly: ['error', 'all'],
-    eqeqeq: 'error',
+    eqeqeq: ['error', 'smart'],
     'prefer-arrow-callback': 'error'
   }
 };
diff --git a/package.json b/package.json
@@ -68,6 +68,7 @@
     "@jupyterlab/builder": "^3.0.0",
     "@jupyterlab/cells": "^3.0.0",
     "@jupyterlab/docregistry": "^3.0.11",
+    "@jupyterlab/fileeditor": "^3.0.11",
     "@jupyterlab/notebook": "^3.0.11",
     "@jupyterlab/statedb": "^3.0.6",
     "@jupyterlab/statusbar": "^3.0.9",

diff --git a/schema/plugin.json b/schema/plugin.json
@@ -19,6 +19,21 @@
       "command": "cm:update-references",
       "keys": ["Alt U"],
       "selector": ".jp-Notebook"
+    },
+    {
+      "command": "cm:insert-citation",
+      "keys": ["Alt C"],
+      "selector": ".jp-FileEditor"
+    },
+    {
+      "command": "cm:insert-bibliography",
+      "keys": ["Alt B"],
+      "selector": ".jp-FileEditor"
+    },
+    {
+      "command": "cm:update-references",
+      "keys": ["Alt U"],
+      "selector": ".jp-FileEditor"
     }
   ],
   "jupyter.lab.setting-icon": "citation:bibliography",

diff --git a/src/adapters/editor.ts b/src/adapters/editor.ts
@@ -0,0 +1,162 @@
+import { IDocumentWidget } from '@jupyterlab/docregistry';
+import { FileEditor } from '@jupyterlab/fileeditor';
+import { CodeEditor } from '@jupyterlab/codeeditor';
+
+import {
+  CitationInsertData,
+  CitationQuerySubset,
+  CiteProc,
+  ICitableItemRecordsBySource,
+  ICitation,
+  ICitationFormattingOptions,
+  IDocumentAdapter
+} from '../types';
+import OutputMode = CiteProc.OutputMode;
+import { HTMLFormatter, TexFormatter, IOutputFormatter } from '../formatting';
+
+
+function editorContentSubset(editor: CodeEditor.IEditor, subset: CitationQuerySubset): string {
+  const cursor = editor.getCursorPosition();
+  const offset = editor.getOffsetAt(cursor);
+  const content = editor.model.value.text;
+  switch (subset) {
+    case 'all':
+      return content;
+    case 'after-cursor':
+      return content.substring(offset);
+    case 'before-cursor':
+      return content.substring(0, offset);
+  }
+}
+
+export class EditorAdapter implements
+  IDocumentAdapter<IDocumentWidget<FileEditor>>
+{
+  citations: ICitation[];
+
+  constructor(
+    public document: IDocumentWidget<FileEditor>,
+    public options: ICitationFormattingOptions
+  ) {
+    this.citations = [];
+  }
+
+  getCitableItemsFallbackData(): ICitableItemRecordsBySource | null {
+    // currently not supported for editors
+    return null;
+  }
+
+  setCitableItemsFallbackData(data: ICitableItemRecordsBySource): void {
+    // currently not supported for editors
+  }
+
+  isAvailable(): boolean {
+    return this.outputFormat === 'latex';
+  }
+
+  private insertAtCursor(text: string) {
+    const fileEditor = this.document.content;
+    if (fileEditor) {
+      const editor = fileEditor.editor;
+      const cursor = editor.getCursorPosition();
+      const offset = editor.getOffsetAt(cursor);
+      fileEditor.model.value.insert(offset, text);
+      const updatedPosition = editor.getPositionAt(offset + text.length);
+      if (updatedPosition) {
+        editor.setCursorPosition(updatedPosition);
+      }
+    }
+  }
+
+  get outputFormat(): OutputMode {
+    // TODO: app.docRegistry.getFileTypeForModel(contentsModel)
+    const codeMirrorMimeType = this.document.content.model.mimeType;
+    if (codeMirrorMimeType === 'text/html') {
+      return 'html';
+    } else if (['text/x-latex', 'text/x-tex'].includes(codeMirrorMimeType)) {
+      return 'latex';
+    } else {
+      return this.options.defaultFormat;
+    }
+  }
+
+  getCitationStyle(): string | undefined {
+    // TODO
+    return;
+  }
+
+  setCitationStyle(newStyle: string): void {
+    // TODO - as metadata in frontmatter for Markdown?
+    return;
+  }
+
+  protected get formatter(): IOutputFormatter {
+    if (this.outputFormat === 'latex') {
+      return new TexFormatter(this.options);
+    }
+    return new HTMLFormatter(this.options);
+  }
+
+  insertBibliography(bibliography: string): void {
+    this.insertAtCursor(this.formatBibliography(bibliography));
+  }
+
+  formatBibliography(bibliography: string): string {
+    return this.formatter.formatBibliography(bibliography);
+  }
+
+  updateBibliography(bibliography: string): void {
+    const newText = this.formatter.updateBibliography(
+      this.document.content.model.value.text,
+      bibliography
+    );
+    if (newText != null) {
+      this.document.content.model.value.text = newText;
+    }
+  }
+
+  formatCitation(citation: CitationInsertData): string {
+    return this.formatter.formatCitation(citation);
+  }
+
+  insertCitation(citation: CitationInsertData): void {
+    this.insertAtCursor(this.formatCitation(citation));
+    // TODO: maybe store current citations in metadata (how?)
+  }
+
+  updateCitation(citation: ICitation): void {
+    const oldText = this.document.content.model.value.text;
+    const { newText, matchesCount } = this.formatter.updateCitation(
+      oldText,
+      citation
+    )
+    if (newText != null) {
+      this.document.content.model.value.text = newText;
+    }
+    if (matchesCount === 0) {
+      console.warn('Failed to update citation', citation, '- no matches found');
+    } else if (matchesCount > 1) {
+      console.warn(
+        'Citation',
+        citation,
+        'appears in more than once with the same ID; please correct it manually'
+      );
+    }
+  }
+
+  findCitations(subset: CitationQuerySubset): ICitation[] {
+
+    const fileEditor = this.document.content;
+    if (!fileEditor) {
+      throw Error('Editor not available')
+    }
+    const editor = fileEditor.editor;
+    return this.formatter.extractCitations(
+      editorContentSubset(editor, subset),
+      {
+        host: this.document.content.node
+      },
+      {}
+    );
+  }
+}
diff --git a/src/adapters/notebook.ts b/src/adapters/notebook.ts
@@ -15,13 +15,12 @@ import type { INotebookModel, NotebookPanel } from '@jupyterlab/notebook';
 import { DocumentRegistry } from '@jupyterlab/docregistry';
 import { DisposableDelegate, IDisposable } from '@lumino/disposable';
 import { CommandToolbarButton } from '@jupyterlab/apputils';
-import { extractCitations } from '../utils';
 import { JupyterFrontEnd } from '@jupyterlab/application';
 import { ReadonlyPartialJSONObject } from '@lumino/coreutils';
 import ICellMetadata = NotebookAdapter.ICellMetadata;
 import type { Cell } from '@jupyterlab/cells';
 import OutputMode = CiteProc.OutputMode;
-import { itemIdToPrimitive } from '../index';
+import { HTMLFormatter, HybridFormatter, IOutputFormatter } from '../formatting';
 
 export namespace NotebookAdapter {
   export interface INotebookMetadata extends ReadonlyPartialJSONObject {
@@ -50,6 +49,7 @@ export namespace NotebookAdapter {
 export const notebookMetadataKey = 'citation-manager';
 export const cellMetadataKey = 'citation-manager';
 
+
 export class NotebookAdapter implements IDocumentAdapter<NotebookPanel> {
   citations: ICitation[];
 
@@ -71,12 +71,16 @@ export class NotebookAdapter implements IDocumentAdapter<NotebookPanel> {
     this.updateCellMetadata();
   }
 
+  isAvailable(): boolean {
+    return true;
+  }
+
   private insertAtCursor(text: string) {
     const activeCell = this.document.content.activeCell;
     if (activeCell) {
-      const cursor = activeCell.editor.getCursorPosition();
-      const offset = activeCell.editor.getOffsetAt(cursor);
       const editor = activeCell.editor;
+      const cursor = editor.getCursorPosition();
+      const offset = editor.getOffsetAt(cursor);
       activeCell.model.value.insert(offset, text);
       const updatedPosition = editor.getPositionAt(offset + text.length);
       if (updatedPosition) {
@@ -155,37 +159,23 @@ export class NotebookAdapter implements IDocumentAdapter<NotebookPanel> {
     });
   }
 
+  protected get formatter(): IOutputFormatter {
+    if (this.outputFormat === 'latex') {
+      return new HybridFormatter(this.options);
+    }
+    return new HTMLFormatter(this.options);
+  }
+
   insertBibliography(bibliography: string): void {
     this.insertAtCursor(this.formatBibliography(bibliography));
   }
 
   formatBibliography(bibliography: string): string {
-    console.log('format', this.outputFormat);
-    if (this.outputFormat === 'latex') {
-      return bibliography;
-    }
-    return `<!-- BIBLIOGRAPHY START -->${bibliography}<!-- BIBLIOGRAPHY END -->`;
+    return this.formatter.formatBibliography(bibliography)
   }
 
   formatCitation(citation: CitationInsertData): string {
-    // note: not using `wrapCitationEntry` as that was causing more problems
-    // (itemID undefined).
-    let text = citation.text;
-    if (this.outputFormat === 'html' && this.options.linkToBibliography) {
-      // link to the first mentioned element
-      const first = citation.items[0];
-      const firstID = itemIdToPrimitive(first);
-      // encode the link as pipe symbol was causing issues with markdown tables,
-      // see https://github.com/krassowski/jupyterlab-citation-manager/issues/50
-      const encodedfirstID = encodeURIComponent(firstID);
-      text = `<a href="#${encodedfirstID}">${text}</a>`;
-    } else if (this.outputFormat === 'latex') {
-      // this does not work well with MathJax - we need to figure out something else!
-      // but it might still be useful (without $) for text editor adapter
-      // const citationIDs = citation.items.map(itemIdToPrimitive).join(',');
-      // text = `$$\\cite{${citationIDs}}$$`;
-    }
-    return `<cite id="${citation.citationId}">${text}</cite>`;
+    return this.formatter.formatCitation(citation)
   }
 
   insertCitation(citation: CitationInsertData): void {
@@ -194,6 +184,7 @@ export class NotebookAdapter implements IDocumentAdapter<NotebookPanel> {
     if (!activeCell) {
       return;
     }
+    // TODO: maybe store current citations in metadata (how?)
     const old =
       (activeCell.model.metadata.get(cellMetadataKey) as ICellMetadata) || {};
     activeCell.model.metadata.set(cellMetadataKey, {
@@ -205,23 +196,16 @@ export class NotebookAdapter implements IDocumentAdapter<NotebookPanel> {
   }
 
   updateCitation(citation: ICitation): void {
-    const pattern = new RegExp(
-      `<cite id=["']${citation.citationId}["'][^>]*?>([\\s\\S]*?)<\\/cite>`
-    );
     let matches = 0;
     this.nonCodeCells.forEach(cell => {
       const oldText = cell.model.value.text;
-      const matchIndex = oldText.search(pattern);
-      if (matchIndex !== -1) {
-        const newCitation = this.formatCitation(citation);
-        const old = oldText.slice(matchIndex, matchIndex + newCitation.length);
-        if (newCitation !== old) {
-          cell.model.value.text = oldText.replace(
-            pattern,
-            this.formatCitation(citation)
-          );
-        }
-        matches += 1;
+      const { newText, matchesCount } = this.formatter.updateCitation(
+        oldText,
+        citation
+      )
+      matches += matchesCount;
+      if (newText != null) {
+        cell.model.value.text = newText;
       }
     });
     if (matches === 0) {
@@ -236,45 +220,13 @@ export class NotebookAdapter implements IDocumentAdapter<NotebookPanel> {
   }
 
   updateBibliography(bibliography: string): void {
-    const htmlPattern =
-      /(?<=<!-- BIBLIOGRAPHY START -->)([\s\S]*?)(?=<!-- BIBLIOGRAPHY END -->)/;
-    const htmlFullyCapturingPattern =
-      /(<!-- BIBLIOGRAPHY START -->[\s\S]*?<!-- BIBLIOGRAPHY END -->)/;
-    const latexPattern =
-      /(\\begin{thebibliography}[\s\S]*?\\end{thebibliography})/;
-
     this.nonCodeCells.forEach(cell => {
-      const oldText = cell.model.value.text;
-      if (oldText.match(/<!-- BIBLIOGRAPHY START -->/)) {
-        cell.model.value.text = oldText.replace(
-          this.outputFormat === 'latex'
-            ? htmlFullyCapturingPattern
-            : htmlPattern,
-          this.outputFormat === 'latex' ? bibliography.trim() : bibliography
-        );
-        if (oldText.search(htmlPattern) === -1) {
-          console.warn(
-            'Failed to update bibliography',
-            bibliography,
-            'in',
-            oldText
-          );
-        }
-      } else if (oldText.match(/\\begin{thebibliography}/)) {
-        cell.model.value.text = oldText.replace(
-          latexPattern,
-          this.outputFormat !== 'latex'
-            ? this.formatBibliography(bibliography)
-            : bibliography.trim()
-        );
-        if (oldText.search(latexPattern) === -1) {
-          console.warn(
-            'Failed to update bibliography',
-            bibliography,
-            'in',
-            oldText
-          );
-        }
+      const newText = this.formatter.updateBibliography(
+        cell.model.value.text,
+        bibliography
+      );
+      if (newText != null) {
+        cell.model.value.text = newText;
       }
     });
   }
@@ -305,7 +257,7 @@ export class NotebookAdapter implements IDocumentAdapter<NotebookPanel> {
       const cellMetadata = cell.model.metadata.get(cellMetadataKey) as
         | NotebookAdapter.ICellMetadata
         | undefined;
-      const cellCitations = extractCitations(
+      const cellCitations = this.formatter.extractCitations(
         cell.model.value.text,
         {
           host: cell.node