fix: molfiles were not correctly placed

zakodium · Apr 4, 2024 · b0a67b8 · b0a67b8
1 parent 91fc857
commit b0a67b8
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Showing 6 changed files with 47 additions and 49 deletions.
diff --git a/src/__tests__/createGeneralTOC.test.js b/src/__tests__/createGeneralTOC.test.js
@@ -17,5 +17,5 @@ test('createGeneralTOC', async () => {
     .map((file) => {
       return statSync(file).size;
     });
-  expect(sizes).toStrictEqual([2211, 404, 899, 483, 250]);
+  expect(sizes).toStrictEqual([1221, 384, 566, 483, 250]);
 });
diff --git a/src/__tests__/general/Data3/index.json b/src/__tests__/general/Data3/index.json
@@ -6,25 +6,20 @@
       },
       "display": {
         "name": "1h.jdx"
-      },
-      "molecules": [
-        {
-          "molfile": "\n  ChemDraw05122111362D\n\n  9  9  0  0  0  0  0  0  0  0999 V2000\n   -0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4125    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4125    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8250   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4125   -1.7862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8250    1.7862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  4  0      \n  2  3  4  0      \n  3  4  4  0      \n  4  5  4  0      \n  5  6  4  0      \n  6  1  4  0      \n  1  7  1  0      \n  7  8  1  0      \n  5  9  1  0      \nM  END\n"
-        }
-      ]
+      }
     },
     {
       "source": {
         "jcampURL": "./cosy.jdx"
       },
       "display": {
         "name": "cosy.jdx"
-      },
-      "molecules": [
-        {
-          "molfile": "\n  ChemDraw05122111362D\n\n  9  9  0  0  0  0  0  0  0  0999 V2000\n   -0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4125    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4125    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8250   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4125   -1.7862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8250    1.7862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  4  0      \n  2  3  4  0      \n  3  4  4  0      \n  4  5  4  0      \n  5  6  4  0      \n  6  1  4  0      \n  1  7  1  0      \n  7  8  1  0      \n  5  9  1  0      \nM  END\n"
-        }
-      ]
+      }
+    }
+  ],
+  "molecules": [
+    {
+      "molfile": "\n  ChemDraw05122111362D\n\n  9  9  0  0  0  0  0  0  0  0999 V2000\n   -0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4125   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4125    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4125    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8250    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8250   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4125   -1.7862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8250    1.7862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  4  0      \n  2  3  4  0      \n  3  4  4  0      \n  4  5  4  0      \n  5  6  4  0      \n  6  1  4  0      \n  1  7  1  0      \n  7  8  1  0      \n  5  9  1  0      \nM  END\n"
     }
   ]
 }
diff --git a/src/__tests__/general/Group1/Data1/index.json b/src/__tests__/general/Group1/Data1/index.json
@@ -3,12 +3,12 @@
     {
       "source": {
         "jcampURL": "./1h.jdx"
-      },
-      "molecules": [
-        {
-          "molfile": "\n  ChemDraw05122111372D\n\n  2  1  0  0  0  0  0  0  0  0999 V2000\n   -0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3572    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0      \nM  END\n"
-        }
-      ]
+      }
+    }
+  ],
+  "molecules": [
+    {
+      "molfile": "\n  ChemDraw05122111372D\n\n  2  1  0  0  0  0  0  0  0  0999 V2000\n   -0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3572    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0      \nM  END\n"
     }
   ]
 }
diff --git a/src/__tests__/general/Group1/Data2/index.json b/src/__tests__/general/Group1/Data2/index.json
@@ -6,25 +6,20 @@
       },
       "display": {
         "name": "13c.jdx"
-      },
-      "molecules": [
-        {
-          "molfile": "\n  ChemDraw05122111372D\n\n  2  1  0  0  0  0  0  0  0  0999 V2000\n   -0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3572    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0      \nM  END\n"
-        }
-      ]
+      }
     },
     {
       "source": {
         "jcampURL": "./cosy.jdx"
       },
       "display": {
         "name": "cosy.jdx"
-      },
-      "molecules": [
-        {
-          "molfile": "\n  ChemDraw05122111372D\n\n  2  1  0  0  0  0  0  0  0  0999 V2000\n   -0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3572    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0      \nM  END\n"
-        }
-      ]
+      }
+    }
+  ],
+  "molecules": [
+    {
+      "molfile": "\n  ChemDraw05122111372D\n\n  2  1  0  0  0  0  0  0  0  0999 V2000\n   -0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3572    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0      \nM  END\n"
     }
   ]
 }
diff --git a/src/commands/createGeneralTOC.js b/src/commands/createGeneralTOC.js
@@ -5,7 +5,7 @@ import { processGeneralFolder } from './toc/processGeneralFolder.js';
  * Add the links based on all the available toc files
  * @param {string} commandDir
  * @param {object} [options={}]
- * @param {boolean} [options.dataDir]
+ * @param {string} [options.dataDir]
  */
 export async function createGeneralTOC(commandDir, options = {}) {
   return createToc(commandDir, processGeneralFolder, options);

diff --git a/src/commands/toc/processGeneralFolder.js b/src/commands/toc/processGeneralFolder.js
@@ -1,9 +1,10 @@
-import { lstatSync, readFileSync, readdirSync, writeFileSync } from 'fs';
+import { lstatSync, readFileSync, readdirSync, writeFileSync, existsSync } from 'fs';
 import { join } from 'path';
 
 import debugFct from 'debug';
 import { hashElement } from 'folder-hash';
 import { createTree } from 'jcampconverter';
+import YAML from 'yaml';
 
 const debug = debugFct('nmrium.general');
 
@@ -12,10 +13,23 @@ let dataCount = 0;
 
 export async function processGeneralFolder(basename, folder, toc) {
   const currentFolder = join(basename, folder);
-  const entries = readdirSync(currentFolder);
-  const molfileName = readdirSync(currentFolder).filter((file) =>
+
+  const folderConfigFilename = join(currentFolder, 'index.yml');
+  const folderConfig = existsSync(folderConfigFilename)
+    ? YAML.parse(readFileSync(folderConfigFilename, 'utf8'))
+    : {};
+
+  // Loading all the molfiles
+  const molfileNames = readdirSync(currentFolder).filter((file) =>
     file.toLowerCase().endsWith('.mol'),
-  )[0];
+  );
+  const molecules = [];
+  for (let molfileName of molfileNames) {
+    const molfile = readFileSync(join(currentFolder, molfileName), 'utf8');
+    molecules.push({ molfile });
+  }
+
+  const entries = readdirSync(currentFolder);
   const spectra = [];
   // we process only the folder if there is an answer (structure.mol)
   const id = (
@@ -32,7 +46,6 @@ export async function processGeneralFolder(basename, folder, toc) {
     const jcampText = readFileSync(join(currentFolder, filename));
     const tree = createTree(jcampText, {});
     const title = tree[0]?.title;
-
     const spectrum = {
       source: {
         jcampURL: `./${filename}`,
@@ -45,25 +58,20 @@ export async function processGeneralFolder(basename, folder, toc) {
       };
     }
 
-    if (molfileName) {
-      const molfile = readFileSync(join(currentFolder, molfileName), 'utf8');
-      spectrum.molecules = [{ molfile }];
-    }
     spectra.push(spectrum);
   }
 
   const targetPath = join(basename, folder, 'index.json');
   debug(`Create: ${targetPath}`);
 
-  writeFileSync(targetPath, JSON.stringify({ spectra }, undefined, 2), 'utf8');
+  writeFileSync(targetPath, JSON.stringify({ spectra, molecules }, undefined, 2), 'utf8');
 
-  let title = folder
-    .replace(/^[^/]*\//, '')
-    .replace(/^[0-9]*$/, '')
-    .replace(/^[0-9]*_/, '');
-  if (!title) {
-    title = `Data ${++dataCount}`;
-  }
+  let title = folderConfig.menuLabel ||
+    folder
+      .replace(/^[^/]*\//, '')
+      .replace(/^[0-9]*$/, '')
+      .replace(/^[0-9]*_/, '') ||
+    `Data ${++dataCount}`;
   const tocEntry = {
     id,
     file: `${URL_FOLDER}/${folder}/index.json`,