Merge pull request #5 from asiomchen/dup-names

asiomchen · web-flow · commit 6257ea84b643 · 2026-04-16T17:51:29.000+02:00
CSV loader improvments
diff --git a/docs/features.md b/docs/features.md
@@ -27,12 +27,12 @@
 ## CSV Import
 
 - Command to import CSV files via browser file picker
-- Auto-detects `smiles` column (case-insensitive)
-- Creates one note per row with YAML frontmatter
+- Creates one note per row with YAML frontmatter; notes are named `row_1`, `row_2`, etc.
 - All CSV columns added as frontmatter properties (keys sanitized to lowercase with non-alphanumeric characters replaced by `_`)
 - Generates a `.base` file scoped to the import folder
 - Handles quoted fields and escaped double quotes per RFC 4180
 - No RDKit dependency — SMILES are taken directly from the CSV
+- Select the molecule property in the view options after import
 
 ## Rendering Settings
 
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -34,7 +34,7 @@ export default tseslint.config(
 		},
 	},
 	{
-		files: ['src/__tests__/**/*.ts'],
+		files: ['src/__tests__/**/*.ts', 'tests/**/*.ts'],
 		languageOptions: {
 			globals: {
 				...globals.node,
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,13 +1,13 @@
 {
   "name": "mols2bases",
-  "version": "0.1.1",
+  "version": "0.1.2",
   "description": "Molecule visualization for Bases",
   "main": "main.js",
   "scripts": {
     "dev": "node esbuild.config.mjs",
     "build": "node esbuild.config.mjs production",
-    "lint": "eslint src/",
-    "lint:fix": "eslint --fix src/",
+    "lint": "eslint src/ tests/",
+    "lint:fix": "eslint --fix src/ tests/",
     "format": "prettier --write src/",
     "format:check": "prettier --check src/",
     "test": "vitest run",
diff --git a/src/csv-import.ts b/src/csv-import.ts
@@ -15,7 +15,7 @@ const BATCH_SIZE = 50;
 
 export function parseCsv(text: string): { headers: string[]; rows: Record<string, string>[] } {
   const lines = text.split(/\r?\n/);
-  if (lines.length === 0) return { headers: [], rows: [] };
+  if (lines.length === 0 || lines[0].trim() === '') return { headers: [], rows: [] };
 
   const headers = parseCsvRow(lines[0]);
   const rows: Record<string, string>[] = [];
@@ -84,19 +84,14 @@ export async function importCsv(plugin: Mols2BasesPlugin): Promise<void> {
 
   try {
     const content = await readFileAsText(file);
-    const { headers, rows } = parseCsv(content);
+    const { rows } = parseCsv(content);
 
     if (rows.length === 0) {
       notice.hide();
       new Notice('No data rows found in the CSV file.');
       return;
     }
 
-    // Auto-detect SMILES column (case-insensitive)
-    const smilesHeader = headers.find(
-      (h) => h.toLowerCase() === plugin.settings.csvSmilesField.toLowerCase(),
-    );
-
     notice.setMessage(`Importing ${rows.length} rows...`);
 
     // Create folder based on filename
@@ -108,38 +103,19 @@ export async function importCsv(plugin: Mols2BasesPlugin): Promise<void> {
     }
 
     // Create .base file early so the view populates as notes arrive
-    const baseContent = buildBaseFile(
-      `${folderPath}.base`,
-      smilesHeader ? `note.${plugin.settings.csvSmilesField}` : undefined,
-    );
+    const baseContent = buildBaseFile(`${folderPath}.base`);
     const basePath = normalizePath(`${folderPath}.base`);
     const baseFile = await plugin.app.vault.create(basePath, baseContent);
     await plugin.app.workspace.getLeaf(false).openFile(baseFile);
 
-    // Show warning if no SMILES column was found
-    if (!smilesHeader) {
-      new Notice(
-        `No "${plugin.settings.csvSmilesField}" column found — select the molecule property in the view options.`,
-        5000,
-      );
-    }
-
-    // Find first non-smiles header for note naming
-    const nameHeader = headers.find((h) => h !== smilesHeader);
-
     for (let i = 0; i < rows.length; i++) {
       const row = rows[i];
-      const name = (nameHeader && row[nameHeader]?.trim()) || `row_${i + 1}`;
+      const name = `row_${i + 1}`;
 
-      // Build frontmatter
       const frontmatter: Record<string, string> = {};
-      if (smilesHeader) {
-        frontmatter[smilesHeader] = row[smilesHeader];
-      }
       frontmatter[INTERNAL_KEYS.LINK] = `[[${baseName}.base]]`;
 
       for (const [key, value] of Object.entries(row)) {
-        if (smilesHeader && key === smilesHeader) continue;
         if (!frontmatter[key]) {
           frontmatter[key] = value;
         }
@@ -150,7 +126,6 @@ export async function importCsv(plugin: Mols2BasesPlugin): Promise<void> {
       const finalPath = await uniquePath(plugin.app, notePath);
       await plugin.app.vault.create(finalPath, `---\n${yaml}---\n`);
 
-      // Yield to the event loop after each batch
       if ((i + 1) % BATCH_SIZE === 0) {
         notice.setMessage(`Importing rows... (${i + 1} / ${rows.length})`);
         await sleep(0);
diff --git a/src/sdf-import.ts b/src/sdf-import.ts
@@ -63,14 +63,7 @@ export async function importSdf(plugin: Mols2BasesPlugin): Promise<void> {
     for (let i = 0; i < molecules.length; i++) {
       const mol = molecules[i];
       const molblockTitle = mol.molblock.split('\n', 1)[0].trim();
-      const name =
-        molblockTitle ||
-        mol.properties.Name ||
-        mol.properties.name ||
-        mol.properties.COMMON_NAME ||
-        mol.properties.ID ||
-        mol.properties.id ||
-        `molecule_${i + 1}`;
+      const name = molblockTitle || `molecule_${i + 1}`;
 
       // Convert MOL block to SMILES via RDKit
       let smiles = '';
diff --git a/src/settings-tab.ts b/src/settings-tab.ts
@@ -133,17 +133,5 @@ export class Mols2BasesSettingTab extends PluginSettingTab {
           await this.plugin.saveSettings();
         }),
       );
-
-    new Setting(containerEl)
-      .setName('CSV SMILES field name')
-      .setDesc('Name of the frontmatter property to use for SMILES when importing CSV files.')
-      .addText((text) =>
-        text.setValue(this.plugin.settings.csvSmilesField).onChange(async (value) => {
-          if (value.trim()) {
-            this.plugin.settings.csvSmilesField = value.trim();
-            await this.plugin.saveSettings();
-          }
-        }),
-      );
   }
 }
diff --git a/src/types.ts b/src/types.ts
@@ -16,7 +16,6 @@ export interface Mols2BasesSettings {
   bondLineWidth: number;
   transparentBg: boolean;
   comicMode: boolean;
-  csvSmilesField: string;
 }
 
 export const DEFAULT_SETTINGS: Mols2BasesSettings = {
@@ -30,7 +29,6 @@ export const DEFAULT_SETTINGS: Mols2BasesSettings = {
   bondLineWidth: 1.0,
   transparentBg: false,
   comicMode: false,
-  csvSmilesField: 'smiles',
 };
 
 export const CONFIG_KEYS = {
diff --git a/tests/csv-parser.test.ts b/tests/csv-parser.test.ts
@@ -0,0 +1,39 @@
+import { describe, it, expect } from 'vitest';
+import { parseCsv } from '../src/csv-import';
+
+describe('parseCsv – basic parsing', () => {
+  it('returns headers and row values', () => {
+    const { headers, rows } = parseCsv('name,smiles\naspirin,CC(=O)Oc1ccccc1C(=O)O');
+    expect(headers).toEqual(['name', 'smiles']);
+    expect(rows).toHaveLength(1);
+    expect(rows[0]).toEqual({ name: 'aspirin', smiles: 'CC(=O)Oc1ccccc1C(=O)O' });
+  });
+
+  it('skips blank lines between data rows', () => {
+    const { rows } = parseCsv('name,smiles\n\naspirin,CCO\n\n');
+    expect(rows).toHaveLength(1);
+  });
+
+  it('returns empty headers and rows for empty input', () => {
+    const { headers, rows } = parseCsv('');
+    expect(headers).toEqual([]);
+    expect(rows).toHaveLength(0);
+  });
+});
+
+describe('parseCsv – RFC 4180 quoting', () => {
+  it('treats a quoted field containing a comma as one field', () => {
+    const { rows } = parseCsv('name,note\naspirin,"painkiller, fever reducer"');
+    expect(rows[0]['note']).toBe('painkiller, fever reducer');
+  });
+
+  it('unescapes doubled quotes inside a quoted field', () => {
+    const { rows } = parseCsv('name,note\ntest,"say ""hello"""');
+    expect(rows[0]['note']).toBe('say "hello"');
+  });
+
+  it('empty trailing field is empty string', () => {
+    const { rows } = parseCsv('a,b,c\n1,2,');
+    expect(rows[0]['c']).toBe('');
+  });
+});
diff --git a/tests/data/dup_names.sdf b/tests/data/dup_names.sdf
@@ -0,0 +1,36 @@
+compound
+  -INDIGO-04142622472D
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+   10.1348   -5.5001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.8652   -5.4996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.0016   -5.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.8652   -6.5005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.1348   -6.5050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.0038   -7.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  3  1  2  0  0  0  0
+  1  5  1  0  0  0  0
+  5  6  2  0  0  0  0
+  6  4  1  0  0  0  0
+  4  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+M  END
+$$$$
+compound
+  -INDIGO-04
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+   10.1348   -5.5001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.8652   -5.4996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.0016   -5.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.8652   -6.5005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.1348   -6.5050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.0038   -7.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  3  1  2  0  0  0  0
+  1  5  1  0  0  0  0
+  5  6  2  0  0  0  0
+  6  4  1  0  0  0  0
+  4  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+M  END
+$$$$
diff --git a/tests/data/missing_names.sdf b/tests/data/missing_names.sdf
diff --git a/tests/data/no_name_at_all.sdf b/tests/data/no_name_at_all.sdf
diff --git a/tests/import-utils.test.ts b/tests/import-utils.test.ts
@@ -1,5 +1,5 @@
 import { describe, it, expect } from 'vitest';
-import { buildYaml } from '../import-utils';
+import { buildYaml, uniquePath } from '../src/import-utils';
 
 // Minimal molblock fragments used across tests
 const HEADER_LINE = ' -OEChem-04032607062D';
@@ -78,3 +78,26 @@ describe('buildYaml – frontmatter round-trip for missing_names.sdf molecules',
     expect(yaml).not.toContain('|2-');
   });
 });
+
+describe('uniquePath – deduplication', () => {
+  const mockApp = (existing: string[]) =>
+    ({ vault: { adapter: { exists: async (p: string) => existing.includes(p) } } }) as never;
+
+  it('returns the path unchanged when it does not exist', async () => {
+    const result = await uniquePath(mockApp([]), 'folder/mol.md');
+    expect(result).toBe('folder/mol.md');
+  });
+
+  it('appends _1 when the base path is taken', async () => {
+    const result = await uniquePath(mockApp(['folder/mol.md']), 'folder/mol.md');
+    expect(result).toBe('folder/mol_1.md');
+  });
+
+  it('increments past _1 when both base and _1 are taken', async () => {
+    const result = await uniquePath(
+      mockApp(['folder/mol.md', 'folder/mol_1.md']),
+      'folder/mol.md',
+    );
+    expect(result).toBe('folder/mol_2.md');
+  });
+});
diff --git a/tests/mocks/obsidian.ts b/tests/mocks/obsidian.ts
@@ -0,0 +1,17 @@
+// Mock obsidian module for testing
+export const Notice = class {
+  constructor(message?: string, duration?: number) {
+    // No-op
+  }
+  hide() {
+    // No-op
+  }
+  setMessage(message: string) {
+    // No-op
+    return this;
+  }
+};
+
+export function normalizePath(path: string): string {
+  return path.replace(/\\/g, '/');
+}
diff --git a/tests/sdf-parser.test.ts b/tests/sdf-parser.test.ts
@@ -1,12 +1,12 @@
 import { readFileSync } from 'fs';
 import { join } from 'path';
 import { describe, it, expect } from 'vitest';
-import { parseSdf } from '../sdf-parser';
+import { parseSdf } from '../src/sdf-parser';
 
-const SDF_PATH = join(__dirname, '..', '..', 'missing_names.sdf');
+const SDF_PATH = join(__dirname, 'data', 'missing_names.sdf');
 const sdfContent = readFileSync(SDF_PATH, 'utf-8');
 
-const NO_NAME_PATH = join(__dirname, '..', '..', 'no_name_at_all.sdf');
+const NO_NAME_PATH = join(__dirname, 'data', 'no_name_at_all.sdf');
 const noNameContent = readFileSync(NO_NAME_PATH, 'utf-8');
 
 describe('parseSdf – missing_names.sdf', () => {
@@ -76,3 +76,27 @@ describe('parseSdf – no_name_at_all.sdf', () => {
     }
   });
 });
+
+const DUP_PATH = join(__dirname, 'data', 'dup_names.sdf');
+const dupContent = readFileSync(DUP_PATH, 'utf-8');
+
+describe('parseSdf – dup_names.sdf', () => {
+  const mols = parseSdf(dupContent);
+
+  it('parses exactly 2 molecules', () => {
+    expect(mols).toHaveLength(2);
+  });
+
+  it('both molecules have molblock title "compound"', () => {
+    for (const mol of mols) {
+      const firstLine = mol.molblock.split('\n')[0];
+      expect(firstLine).toBe('compound');
+    }
+  });
+
+  it('both molecules contain M  END', () => {
+    for (const mol of mols) {
+      expect(mol.molblock).toContain('M  END');
+    }
+  });
+});
diff --git a/tsconfig.json b/tsconfig.json
@@ -14,5 +14,5 @@
     "outDir": "./dist",
     "skipLibCheck": true
   },
-  "include": ["src/**/*.ts"]
+  "include": ["src/**/*.ts", "tests/**/*.ts"]
 }
diff --git a/vitest.config.ts b/vitest.config.ts
@@ -0,0 +1,12 @@
+import { defineConfig } from 'vitest/config';
+
+export default defineConfig({
+  test: {
+    globals: true,
+  },
+  resolve: {
+    alias: {
+      obsidian: new URL('./tests/mocks/obsidian.ts', import.meta.url).pathname,
+    },
+  },
+});

Original file line number	Diff line number	Diff line change
`@@ -34,7 +34,7 @@ export default tseslint.config(`
`34`	`34`	`},`
`35`	`35`	`},`
`36`	`36`	`{`
`37`		`- files: ['src/__tests__/*/.ts'],`
	`37`	`+ files: ['src/__tests__/*/.ts', 'tests/*/.ts'],`
`38`	`38`	`languageOptions: {`
`39`	`39`	`globals: {`
`40`	`40`	`...globals.node,`