Add NMIND data

nmind · Feb 13, 2024 · a41dfcd · a41dfcd
1 parent e3fd0e4
commit a41dfcd
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Showing 65 changed files with 563 additions and 7,898 deletions.
diff --git a/package.json b/package.json
@@ -3,12 +3,12 @@
 	"version": "0.0.1",
 	"private": true,
 	"scripts": {
-		"dev": "node src/lib/data/concatenate_data.js src/lib/data/evaluatedTools src/lib/data/evaluationSchemas src/lib/data/concat_data.json && vite dev",
-		"build": "node src/lib/data/concatenate_data.js src/lib/data/evaluatedTools src/lib/data/evaluationSchemas src/lib/data/concat_data.json && vite build",
+		"dev": "node src/lib/data/back_migrate_tools.js && node src/lib/data/concatenate_data.js src/lib/data/evaluatedTools src/lib/data/evaluationSchemas src/lib/data/concat_data.json && vite dev",
+		"build": "node src/lib/data/back_migrate_tools.js && node src/lib/data/concatenate_data.js src/lib/data/evaluatedTools src/lib/data/evaluationSchemas src/lib/data/concat_data.json && vite build",
 		"preview": "vite preview",
 		"check": "svelte-kit sync && svelte-check --tsconfig ./tsconfig.json",
 		"check:watch": "svelte-kit sync && svelte-check --tsconfig ./tsconfig.json --watch",
-		"build_test_fixtures": "node src/lib/data/concatenate_data.js tests/fixtures/evaluatedTools tests/fixtures/evaluationSchemas src/lib/data/concat_data.json",
+		"build_test_fixtures": "node src/lib/data/back_migrate_tools.js && node src/lib/data/concatenate_data.js tests/fixtures/evaluatedTools tests/fixtures/evaluationSchemas src/lib/data/concat_data.json",
 		"test": "vitest",
 		"lint": "prettier --plugin-search-dir . --check . && eslint .",
 		"format": "prettier --plugin-search-dir . --write ."

diff --git a/src/lib/data/back_migrate_tools.js b/src/lib/data/back_migrate_tools.js
@@ -0,0 +1,106 @@
+// @ts-nocheck
+import { promises } from 'fs';
+import { join } from 'path';
+
+const PATH_DIR_ENTRIES_INPUT = 'src/lib/data/entries';
+const PATH_DIR_ENTRIES_OUTPUT = 'src/lib/data/evaluatedTools';
+
+
+const OUTPUT_SKELETON = {
+	"name": null,
+	"description": null,
+	"urls": [],
+	"maintainers": [],
+	"evaluations": [],
+	"slug": null,
+	"image": "brain_9_svgrepo_com--CadetBlue.png",
+	"tags": []
+};
+
+const EVALUATION_SKELETON = {
+	"checklistVersion": "1.1",
+	"toolVersion": "0.0.0",
+	"date": null,
+	"evaluatorEmail": "[email protected]",
+	"checklist": {}
+}
+
+
+/**
+ * Read all json files from the input directory
+ * @param {string} dirPath - The path to the directory to read from
+ * @returns {Promise<any[]>} Each element is the parsed JSON content of a file
+ */
+async function readDirectoryData(dirPath) {
+	const files = await promises.readdir(dirPath);
+	const jsonFiles = files.filter((file) => file.endsWith('.json'));
+
+	return Promise.all(
+		jsonFiles.map(async (file) => {
+			const filePath = join(dirPath, file);
+			try {
+				const fileContents = await promises.readFile(filePath, 'utf8');
+				return JSON.parse(fileContents);
+			} catch (error) {
+				console.error(`Error reading file ${filePath}:`, error.message);
+				throw error;
+			}
+		})
+	);
+}
+
+function makeUrlSafeName(name) {
+	return name.toLowerCase().replace(/[^\w\s]/gi, '').replace(/ /g, '-');
+}
+
+function convertKeys(obj) {
+    const newObj = {};
+    Object.keys(obj).forEach(key => {
+        let categoryAbbreviation;
+        if (key === 'testing') {
+            categoryAbbreviation = 'tst';
+        } else if (key === 'infrastructure') {
+            categoryAbbreviation = 'inf';
+        } else if (key === 'documentation') {
+            categoryAbbreviation = 'doc';
+        } else {
+			return;
+		}
+        newObj[key] = {};
+        Object.keys(obj[key]).forEach(subKey => {
+			newObj[key][subKey] = {};
+			Object.keys(obj[key][subKey]).forEach(subSubKey => {
+				newObj[key][subKey][`${subKey}_${categoryAbbreviation}_${subSubKey}`] = obj[key][subKey][subSubKey];
+			});
+        });
+    });
+    return newObj;
+}
+
+function backMigrate(entry) {
+	const entry_backmigrated = { ...OUTPUT_SKELETON };
+	entry_backmigrated.name = entry.name;
+	entry_backmigrated.description = `This tool was migrated from the old format. Please update it.`;
+	entry_backmigrated.urls = entry.urls.map(x => ({ "text": x.url_type, href: x.url }));
+	entry_backmigrated.slug = makeUrlSafeName(entry.name);
+
+	const evaluation = { ...EVALUATION_SKELETON };
+	// set date as today in the format YYYY-MM-DD
+	evaluation.date = new Date().toISOString().split('T')[0];
+	evaluation.checklist = convertKeys(entry);
+
+	entry_backmigrated.evaluations.push(evaluation);
+	return entry_backmigrated;
+}
+
+// Create the output directory if it doesn't exist
+await promises.mkdir(PATH_DIR_ENTRIES_OUTPUT, { recursive: true });
+
+// Read all entries from the input directory, and write them to the output directory
+for (const entry of await readDirectoryData(PATH_DIR_ENTRIES_INPUT)) {
+	const entry_backmigrated = backMigrate(entry);
+	const id = entry_backmigrated.slug;
+	const outputPath = join(PATH_DIR_ENTRIES_OUTPUT, `${id}.json`);
+	await promises.writeFile(outputPath, JSON.stringify(entry_backmigrated, null, 2));
+	console.log(`Generated ${outputPath} successfully.`);
+}
diff --git a/src/lib/data/entries/checklist_C_PAC.json b/src/lib/data/entries/checklist_C_PAC.json
@@ -0,0 +1,79 @@
+{
+  "name": "C-PAC",
+  "urls": [
+    {
+      "url_type": "Source code",
+      "url": "https://github.com/FCP-INDI/C-PAC"
+    },
+    {
+      "url_type": "Landing page",
+      "url": "https://fcp-indi.github.io/"
+    }
+  ],
+  "documentation": {
+    "bronze": {
+      "1": true,
+      "2": false,
+      "3": false,
+      "4": true,
+      "5": true,
+      "6": true,
+      "7": true,
+      "8": true,
+      "9": true
+    },
+    "silver": {
+      "1": true,
+      "2": false,
+      "3": true,
+      "4": true,
+      "5": true,
+      "6": true
+    },
+    "gold": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": false,
+      "6": false
+    }
+  },
+  "infrastructure": {
+    "bronze": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": true,
+      "6": false,
+      "7": true
+    },
+    "silver": {
+      "1": true,
+      "2": true,
+      "3": true
+    },
+    "gold": {
+      "1": true,
+      "2": false,
+      "3": false,
+      "4": false,
+      "5": false
+    }
+  },
+  "testing": {
+    "bronze": {
+      "1": true,
+      "2": true
+    },
+    "silver": {
+      "1": true,
+      "2": false
+    },
+    "gold": {
+      "1": false,
+      "2": false
+    }
+  }
+}
diff --git a/src/lib/data/entries/checklist_DataLad.json b/src/lib/data/entries/checklist_DataLad.json
@@ -0,0 +1,75 @@
+{
+  "name": "DataLad",
+  "urls": [
+    {
+      "url_type": "Source code",
+      "url": "https://github.com/datalad/datalad/"
+    }
+  ],
+  "documentation": {
+    "bronze": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": true,
+      "6": true,
+      "7": true,
+      "8": true,
+      "9": true
+    },
+    "silver": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": true,
+      "6": true
+    },
+    "gold": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": true,
+      "6": true
+    }
+  },
+  "infrastructure": {
+    "bronze": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": true,
+      "6": true,
+      "7": true
+    },
+    "silver": {
+      "1": true,
+      "2": true,
+      "3": true
+    },
+    "gold": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": true
+    }
+  },
+  "testing": {
+    "bronze": {
+      "1": true,
+      "2": true
+    },
+    "silver": {
+      "1": true,
+      "2": true
+    },
+    "gold": {
+      "1": true,
+      "2": true
+    }
+  }
+}
diff --git a/src/lib/data/entries/checklist_dcm2niix.json b/src/lib/data/entries/checklist_dcm2niix.json
@@ -0,0 +1,75 @@
+{
+  "name": "dcm2niix",
+  "urls": [
+    {
+      "url_type": "Source code",
+      "url": "https://github.com/rordenlab/dcm2niix"
+    }
+  ],
+  "documentation": {
+    "bronze": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": true,
+      "6": true,
+      "7": true,
+      "8": true,
+      "9": true
+    },
+    "silver": {
+      "1": true,
+      "2": false,
+      "3": true,
+      "4": true,
+      "5": false,
+      "6": true
+    },
+    "gold": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": false,
+      "5": true,
+      "6": true
+    }
+  },
+  "infrastructure": {
+    "bronze": {
+      "1": true,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": true,
+      "6": false,
+      "7": true
+    },
+    "silver": {
+      "1": true,
+      "2": false,
+      "3": true
+    },
+    "gold": {
+      "1": false,
+      "2": true,
+      "3": true,
+      "4": true,
+      "5": false
+    }
+  },
+  "testing": {
+    "bronze": {
+      "1": true,
+      "2": true
+    },
+    "silver": {
+      "1": true,
+      "2": false
+    },
+    "gold": {
+      "1": false,
+      "2": false
+    }
+  }
+}