Update dependencies and make it works

package.json

@@ -7,35 +7,49 @@
   },
   "bugs": "https://github.com/foambubble/foam/issues",
   "dependencies": {
-    "@oclif/command": "^1",
-    "@oclif/config": "^1",
-    "@oclif/plugin-help": "^3",
-    "foam-core": "^0.11.0",
+    "@oclif/command": "^1.8.16",
+    "@oclif/config": "^1.18.3",
+    "@oclif/plugin-help": "^5.1.12",
+    "detect-newline": "^3.1.0",
+    "fast-array-diff": "^1.0.1",
+    "github-slugger": "^1.4.0",
+    "glob": "^7.1.6",
+    "lodash": "^4.17.21",
+    "micromatch": "^4.0.2",
     "ora": "^4.0.4",
-    "tslib": "^1"
+    "remark-frontmatter": "^2.0.0",
+    "remark-parse": "^8.0.2",
+    "remark-wiki-link": "^0.0.4",
+    "title-case": "^3.0.2",
+    "unified": "^9.0.0",
+    "unist-util-visit": "^2.0.2",
+    "yaml": "^1.10.0"
   },
   "devDependencies": {
-    "@babel/core": "^7.10.4",
-    "@babel/preset-env": "^7.10.4",
-    "@babel/preset-typescript": "^7.10.4",
-    "@oclif/dev-cli": "^1",
-    "@types/node": "^10",
-    "babel-jest": "^26.1.0",
+    "@babel/core": "^7.17.8",
+    "@babel/preset-env": "^7.16.11",
+    "@babel/preset-typescript": "^7.16.7",
+    "@oclif/dev-cli": "^1.26.10",
+    "@types/github-slugger": "^1.3.0",
+    "@types/glob": "^7.1.1",
+    "@types/jest": "^27.4.1",
+    "@types/lodash": "^4.14.157",
+    "@types/micromatch": "^4.0.1",
+    "@types/node": "^13.11.0",
+    "babel-jest": "^27.5.1",
     "chai": "^4",
     "eslint": "^5.13",
     "eslint-config-oclif": "^3.1",
     "eslint-config-oclif-typescript": "^0.1",
     "globby": "^10",
     "jest": "^26.1.0",
     "mock-fs": "^4.12.0",
-    "ts-node": "^8",
+    "ts-node": "^10.7.0",
+    "tslib": "^2.3.1",
     "typescript": "^3.3"
   },
-  "peerDependencies": {
-    "foam-core": "*"
-  },
   "engines": {
-    "node": ">=12.0.0"
+    "node": ">=16.0.0"
   },
   "files": [
     "/bin",
@@ -56,7 +70,7 @@
       "@oclif/plugin-help"
     ]
   },
-  "repository": "foambubble/foam",
+  "repository": "foambubble/foam-cli",
   "scripts": {
     "clean": "rimraf tmp",
     "build": "tsc -b",

src/commands/janitor.ts

@@ -1,18 +1,17 @@
 import { Command, flags } from '@oclif/command';
 import ora from 'ora';
-import {
-  bootstrap,
-  createConfigFromFolders,
-  generateLinkReferences,
-  generateHeading,
-  applyTextEdit,
-  FileDataStore,
-  URI,
-  isNote,
-} from 'foam-core';
+import { MarkdownResourceProvider } from "../core/markdown-provider";
+import { bootstrap } from '../core/model/foam';
+import { URI } from '../core/model/uri';
+import { Resource } from '../core/model/note';
+import { generateHeading, generateLinkReferences } from '../core/janitor';
+import { applyTextEdit } from '../core/janitor/apply-text-edit';
+import { FileDataStore, Matcher } from '../core/services/datastore';
 import { writeFileToDisk } from '../utils/write-file-to-disk';
 import { isValidDirectory } from '../utils';
 
+const isNote = (resource: Resource): resource is Resource => resource.type === 'note'
+
 export default class Janitor extends Command {
   static description =
     'Updates link references and heading across all the markdown files in the given workspaces';
@@ -41,8 +40,14 @@ export default class Janitor extends Command {
     const { workspacePath = './' } = args;
 
     if (isValidDirectory(workspacePath)) {
-      const config = createConfigFromFolders([URI.file(workspacePath)]);
-      const workspace = (await bootstrap(config, { dataStore: new FileDataStore(config)}))
+      const matcher = new Matcher(
+        [URI.file(workspacePath)],
+        ['**/*'],
+        []
+      );
+      const dataStore = new FileDataStore();
+      const markdownProvider = new MarkdownResourceProvider(matcher);
+      const workspace = (await bootstrap(matcher, dataStore, [markdownProvider]))
         .workspace;
 
       const notes = workspace.list().filter(isNote);

src/commands/migrate.ts

@@ -1,19 +1,25 @@
+import GithubSlugger from 'github-slugger';
 import { Command, flags } from '@oclif/command';
 import ora from 'ora';
-import {
-  bootstrap,
-  createConfigFromFolders,
-  generateLinkReferences,
-  generateHeading,
-  getKebabCaseFileName,
-  applyTextEdit,
-  FileDataStore,
-  isNote,
-} from 'foam-core';
+import { bootstrap } from '../core/model/foam';
+import { URI } from '../core/model/uri';
+import { Resource } from '../core/model/note';
+import { generateHeading, generateLinkReferences } from '../core/janitor';
+import { applyTextEdit } from '../core/janitor/apply-text-edit';
+import { FileDataStore, Matcher } from '../core/services/datastore';
 import { writeFileToDisk } from '../utils/write-file-to-disk';
 import { renameFile } from '../utils/rename-file';
 import { isValidDirectory } from '../utils';
 
+const slugger = new GithubSlugger();
+
+const isNote = (resource: Resource): resource is Resource => resource.type === 'note'
+
+const getKebabCaseFileName = (fileName: string) => {
+  const kebabCasedFileName = slugger.slug(fileName);
+  return kebabCasedFileName === fileName ? null : kebabCasedFileName;
+};
+
 // @todo: Refactor 'migrate' and 'janitor' commands and avoid repeatition
 export default class Migrate extends Command {
   static description =
@@ -42,11 +48,16 @@ Successfully generated link references and heading!
     const { args, flags } = this.parse(Migrate);
 
     const { workspacePath = './' } = args;
-    const config = createConfigFromFolders([workspacePath]);
+
+    const matcher = new Matcher(
+      [URI.file(workspacePath)],
+      ['**/*'],
+      []
+    );
+    const dataStore = new FileDataStore();
 
     if (isValidDirectory(workspacePath)) {
-      const dataStore = new FileDataStore(config);
-      let workspace = (await bootstrap(config, { dataStore: dataStore})).workspace;
+      let workspace = (await bootstrap(matcher, dataStore, [])).workspace;
 
       let notes = workspace.list().filter(isNote);
 
@@ -75,7 +86,7 @@ Successfully generated link references and heading!
       spinner.text = 'Renaming files';
 
       // Reinitialize the graph after renaming files
-      workspace = (await bootstrap(config, { dataStore: dataStore})).workspace;
+      workspace = (await bootstrap(matcher, dataStore, [])).workspace;
 
       notes = workspace.list().filter(isNote);
 

src/core/common/snippetParser.ts

@@ -571,7 +571,7 @@ export class TextmateSnippet extends Marker {
 		resolvedVariables.forEach(variable => {
 			result += this.value.substring(i, variable.pos);
 			result += variable.toString();
-			i = variable.endPos;
+			i = variable.endPos ?? i;
 		});
 		result += this.value.substring(i);
 

src/core/janitor/generateLinkReferences.test.ts

@@ -47,9 +47,9 @@ describe('generateLinkReferences', () => {
 
     const actual = generateLinkReferences(note, _workspace, false);
 
-    expect(actual!.range.start).toEqual(expected.range.start);
-    expect(actual!.range.end).toEqual(expected.range.end);
-    expect(actual!.newText).toEqual(expected.newText);
+    expect(actual?.range.start).toEqual(expected.range.start);
+    expect(actual?.range.end).toEqual(expected.range.end);
+    expect(actual?.newText).toEqual(expected.newText);
   });
 
   it('should remove link definitions from a file that has them, if no links are present', () => {
@@ -62,9 +62,9 @@ describe('generateLinkReferences', () => {
 
     const actual = generateLinkReferences(note, _workspace, false);
 
-    expect(actual!.range.start).toEqual(expected.range.start);
-    expect(actual!.range.end).toEqual(expected.range.end);
-    expect(actual!.newText).toEqual(expected.newText);
+    expect(actual?.range.start).toEqual(expected.range.start);
+    expect(actual?.range.end).toEqual(expected.range.end);
+    expect(actual?.newText).toEqual(expected.newText);
   });
 
   it('should update link definitions if they are present but changed', () => {
@@ -82,9 +82,9 @@ describe('generateLinkReferences', () => {
 
     const actual = generateLinkReferences(note, _workspace, false);
 
-    expect(actual!.range.start).toEqual(expected.range.start);
-    expect(actual!.range.end).toEqual(expected.range.end);
-    expect(actual!.newText).toEqual(expected.newText);
+    expect(actual?.range.start).toEqual(expected.range.start);
+    expect(actual?.range.end).toEqual(expected.range.end);
+    expect(actual?.newText).toEqual(expected.newText);
   });
 
   it('should not cause any changes if link reference definitions were up to date', () => {
@@ -112,9 +112,9 @@ describe('generateLinkReferences', () => {
 
     const actual = generateLinkReferences(note, _workspace, false);
 
-    expect(actual!.range.start).toEqual(expected.range.start);
-    expect(actual!.range.end).toEqual(expected.range.end);
-    expect(actual!.newText).toEqual(expected.newText);
+    expect(actual?.range.start).toEqual(expected.range.start);
+    expect(actual?.range.end).toEqual(expected.range.end);
+    expect(actual?.newText).toEqual(expected.newText);
   });
 
   it('should not remove explicitly entered link references', () => {
@@ -155,5 +155,5 @@ describe('generateLinkReferences', () => {
  * @param text starting text, using a \n line separator
  */
 function textForNote(note: Resource, text: string): string {
-  return text.split('\n').join(note.source.eol);
+  return text.split('\n').join(note?.source.eol);
 }

src/core/markdown-provider.ts

@@ -239,10 +239,12 @@ const sectionsPlugin: ParserPlugin = {
         sectionStack[sectionStack.length - 1].level >= level
       ) {
         const section = sectionStack.pop();
-        note.sections.push({
-          label: section.label,
-          range: Range.createFromPosition(section.start, start),
-        });
+        if (section) {
+          note.sections.push({
+            label: section.label,
+            range: Range.createFromPosition(section.start, start),
+          });
+        }
       }
 
       // Add the new section to the stack
@@ -254,10 +256,12 @@ const sectionsPlugin: ParserPlugin = {
     // Close all the remainig sections
     while (sectionStack.length > 0) {
       const section = sectionStack.pop();
-      note.sections.push({
-        label: section.label,
-        range: { start: section.start, end },
-      });
+      if (section) {
+        note.sections.push({
+          label: section.label,
+          range: { start: section.start, end },
+        });
+      }
     }
     note.sections.sort((a, b) =>
       Position.compareTo(a.range.start, b.range.start)
@@ -386,7 +390,7 @@ export function createMarkdownParser(
     try {
       plugin.onDidInitializeParser?.(parser);
     } catch (e) {
-      handleError(plugin, 'onDidInitializeParser', undefined, e);
+      handleError(plugin, 'onDidInitializeParser', undefined, e as Error);
     }
   });
 
@@ -397,7 +401,7 @@ export function createMarkdownParser(
         try {
           return plugin.onWillParseMarkdown?.(acc) || acc;
         } catch (e) {
-          handleError(plugin, 'onWillParseMarkdown', uri, e);
+          handleError(plugin, 'onWillParseMarkdown', uri, e as Error);
           return acc;
         }
       }, markdown);
@@ -425,7 +429,7 @@ export function createMarkdownParser(
         try {
           plugin.onWillVisitTree?.(tree, note);
         } catch (e) {
-          handleError(plugin, 'onWillVisitTree', uri, e);
+          handleError(plugin, 'onWillVisitTree', uri, e as Error);
         }
       });
       visit(tree, node => {
@@ -446,7 +450,7 @@ export function createMarkdownParser(
               try {
                 plugins[i].onDidFindProperties?.(yamlProperties, note, node);
               } catch (e) {
-                handleError(plugins[i], 'onDidFindProperties', uri, e);
+                handleError(plugins[i], 'onDidFindProperties', uri, e as Error);
               }
             }
           } catch (e) {
@@ -458,15 +462,15 @@ export function createMarkdownParser(
           try {
             plugins[i].visit?.(node, note, markdown);
           } catch (e) {
-            handleError(plugins[i], 'visit', uri, e);
+            handleError(plugins[i], 'visit', uri, e as Error);
           }
         }
       });
       plugins.forEach(plugin => {
         try {
           plugin.onDidVisitTree?.(tree, note);
         } catch (e) {
-          handleError(plugin, 'onDidVisitTree', uri, e);
+          handleError(plugin, 'onDidVisitTree', uri, e as Error);
         }
       });
       Logger.debug('Result:', note);

src/core/model/graph.ts

@@ -102,9 +102,10 @@ export class FoamGraph implements IDisposable {
     const resourcesToUpdate: URI[] = [];
     for (const placeholderId of this.placeholders.keys()) {
       // quick and dirty check for affected resources
-      if (resource.uri.path.endsWith(placeholderId + '.md')) {
+      const backlink = this.backlinks.get(placeholderId)
+      if (resource.uri.path.endsWith(placeholderId + '.md') && backlink) {
         resourcesToUpdate.push(
-          ...this.backlinks.get(placeholderId).map(c => c.source)
+          ...backlink.map(c => c.source)
         );
         // resourcesToUpdate.push(resource);
       }

src/core/model/workspace.test.ts

@@ -76,7 +76,7 @@ describe('Workspace resources', () => {
       ['note2', '/note2.md'],
     ]) {
       expect(ws.listByIdentifier(reference)[0].uri.path).toEqual(path);
-      expect(ws.find(reference).uri.path).toEqual(path);
+      expect(ws.find(reference)?.uri.path).toEqual(path);
     }
   });
 
@@ -86,7 +86,7 @@ describe('Workspace resources', () => {
       .set(createTestNote({ uri: 'file.md' }));
 
     const res = ws.find('test-file#my-section');
-    expect(res.uri.fragment).toEqual('my-section');
+    expect(res?.uri.fragment).toEqual('my-section');
   });
 });