New project page components

.eslintignore

@@ -1,4 +1,5 @@
 /public/lib/
-/public/js/
+/public/js/*
+!/public/js/surfacenets-worker.js
 dist/
 /view/atlasmaker/src/tools/render3D/three.js*

.eslintrc.js

@@ -2,5 +2,15 @@ module.exports = {
   'env': {
     'mocha': true
   },
-  'extends': ['naat']
+  'extends': ['naat', 'plugin:vue/vue3-strongly-recommended'],
+  'rules': { 'vue/multi-word-component-names': 'off' },
+  'overrides': [
+    {
+      files: ['*.vue'],
+      rules: {
+        // 300 lines limit seems to short for *.vue files
+        'max-lines': 'off'
+      }
+    }
+  ]
 };

.gitignore

@@ -15,14 +15,8 @@ public/_img-all/
 public/.DS_Store
 public/data
 public/doc2/*
-public/js/
-public/js/ask-for-login-page.js
-public/js/index-page.js
-public/js/mri-page.js
-public/js/project-new-page.js
-public/js/project-page.js
-public/js/project-settings-page.js
-public/js/user-page.js
+/public/js/*
+!/public/js/surfacenets-worker.js
 public/lib/.DS_Store
 public/lib/atlasmaker-tools
 public/lib/atlasmaker.js

.vscode/settings.json

@@ -3,7 +3,13 @@
     "editor.formatOnSave": false,
     "editor.codeActionsOnSave": [
       // "source.formatDocument", // problem with switch case multi lines comment indents
-      "source.fixAll.eslint" // used by dbaeumer.vscode-eslint
+      "source.fixAll.eslint"
     ]
+  },
+  "[vue]": {
+    "editor.formatOnSave": false,
+    "editor.codeActionsOnSave": {
+      "source.fixAll.eslint": "explicit"
+    },
   }
-}
+}

app.js

@@ -4,21 +4,21 @@
     Atlas Maker Server
     Roberto Toro, 25 July 2014
 */
-const nwl = require('neuroweblab');
 const fs = require('fs');
-const express = require('express');
-const compression = require('compression');
+const http = require('http');
+const https = require('https');
 const path = require('path');
-const favicon = require('serve-favicon');
-const logger = require('morgan');
-const tracer = require('tracer').console({ format: '[{{file}}:{{line}}]  {{message}}' });
-const cookieParser = require('cookie-parser');
+
 const bodyParser = require('body-parser');
+const compression = require('compression');
+const cookieParser = require('cookie-parser');
+const express = require('express');
+const logger = require('morgan');
 const mustacheExpress = require('mustache-express');
+const nwl = require('neuroweblab');
+const favicon = require('serve-favicon');
+const tracer = require('tracer').console({ format: '[{{file}}:{{line}}]  {{message}}' });
 const Config = JSON.parse(fs.readFileSync('./cfg.json'));
-const https = require('https');
-const http = require('http');
-
 global.authTokenMiddleware = nwl.authTokenMiddleware;
 
 const AtlasmakerServer = require('./controller/atlasmakerServer/atlasmakerServer');
@@ -129,7 +129,7 @@ const start = async function () {
   // Configure server and web socket
   //========================================================================================
 
-  const server = http.createServer(app).listen(3001, () => { console.log('Listening http on port 3001'); });
+  const server = http.createServer(app).listen(Config.app_port, () => { console.log(`Listening http on port ${Config.app_port}`); });
   const atlasmakerServer = new AtlasmakerServer(db);
   atlasmakerServer.dataDirectory = dirname + '/public';
 
@@ -146,11 +146,11 @@ const start = async function () {
     atlasmakerServer.server = http.createServer(app);
   }
 
-  atlasmakerServer.server.listen(8080, () => {
+  atlasmakerServer.server.listen(Config.ws_port, () => {
     if (Config.secure) {
-      console.log('Listening wss on port 8080');
+      console.log(`Listening wss on port ${Config.ws_port}`);
     } else {
-      console.log('Listening ws on port 8080');
+      console.log(`Listening ws on port ${Config.ws_port}`);
     }
     atlasmakerServer.initSocketConnection();
   });

cfg.json.example

@@ -1,6 +1,8 @@
 {
     "hostname": "http://localhost:3001",
-    "wshostname": "localhost:8080",
+    "wshostname": "ws://localhost:8080",
+    "app_port": 3001,
+    "ws_port": 8080,
     "secure": false,
     "ssl_key": "./key.pem",
     "ssl_cert": "./cert.pem",

controller/admin/admin.controller.js

@@ -1,6 +1,7 @@
-const notifier = require('../../notifier');
 const { body, validationResult } = require('express-validator');
 
+const notifier = require('../../notifier');
+
 const validator = (req, res, next) => {
   const authorizedIP = ['1']; // hardcoded authorized IPs
   let ip;

controller/admin/index.js

@@ -1,4 +1,5 @@
 const express = require('express');
+
 const controller = require('./admin.controller');
 const router = new express.Router();
 

controller/api/api.controller.js

@@ -1,5 +1,6 @@
 const fs = require('fs');
 const path = require('path');
+
 const tracer = require('tracer').console({format: '[{{file}}:{{line}}]  {{message}}'});
 
 const getLabelsets = async (req, res) => {
@@ -18,7 +19,7 @@ const getLabelsets = async (req, res) => {
 
 const userNameQuery = (req, res) => {
   const {query} = req;
-  if(typeof query.q === 'undefined') {
+  if (typeof query.q === 'undefined') {
     res.status(400).send({error: 'missing q parameter'});
 
     return;
@@ -27,8 +28,8 @@ const userNameQuery = (req, res) => {
   db.get('user')
     .find(
       { $or: [
-        {nickname: {$regex:query.q}},
-        {name: {$regex:query.q}}
+        {nickname: {$regex: query.q}},
+        {name: {$regex: query.q}}
       ]},
       { fields: ['name', 'nickname'], limit: 10 }
     )
@@ -44,7 +45,7 @@ const userNameQuery = (req, res) => {
 const getAtlasBackups = (req, res) => {
   const { source, atlasProject, atlasName } = req.query;
 
-  if(typeof source === 'undefined'
+  if (typeof source === 'undefined'
       || typeof atlasProject === 'undefined'
       || atlasName === 'undefined') {
     res.status(400);
@@ -59,30 +60,30 @@ const getAtlasBackups = (req, res) => {
   const db = req.app.db.mongoDB();
   db.get('mri').findOne({
     source: source,
-    'mri.atlas': {$elemMatch:{name: atlasName, project: atlasProject}},
+    'mri.atlas': {$elemMatch: {name: atlasName, project: atlasProject}},
     backup: {$exists: 0}
   }, {url: 1, 'mri.atlas.$': 1})
-    .then( (obj) => {
+    .then((obj) => {
     // get all filenames that have ever been associated with this atlas
       let {url: dataDir} = obj;
       [,, dataDir] = dataDir.split('/');
       db.get('mri').aggregate([
-        { $match:{ source: source, 'mri.atlas':{$elemMatch: {project: atlasProject, name: atlasName}}}},
+        { $match: { source: source, 'mri.atlas': {$elemMatch: {project: atlasProject, name: atlasName}}}},
         { $unwind: '$mri.atlas' },
-        { $match: { 'mri.atlas.project':atlasProject, 'mri.atlas.name': atlasName}},
-        { $group: {_id:{filename: '$mri.atlas.filename'}}},
-        { $project: {_id:0, filename:'$_id.filename'}}
+        { $match: { 'mri.atlas.project': atlasProject, 'mri.atlas.name': atlasName}},
+        { $group: {_id: {filename: '$mri.atlas.filename'}}},
+        { $project: {_id: 0, filename: '$_id.filename'}}
       ])
-        .then( (obj2) => {
+        .then((obj2) => {
         // get all backups for those files...
           let i;
           const promiseArray = [];
           // ...from backup logs
-          for(i=0; i<obj2.length; i++) {
+          for (i = 0; i < obj2.length; i++) {
             promiseArray.push(
               db.get('log').aggregate([
-                { $match: {key:'saveAtlasBackup', 'value.atlasDirectory': dataDir, 'value.atlasFilename': obj2[i].filename}},
-                { $project: {_id:0, filename:'$value.atlasFilename', timestamp:'$value.timestamp'}}
+                { $match: {key: 'saveAtlasBackup', 'value.atlasDirectory': dataDir, 'value.atlasFilename': obj2[i].filename}},
+                { $project: {_id: 0, filename: '$value.atlasFilename', timestamp: '$value.timestamp'}}
               ])
             );
           }
@@ -92,23 +93,23 @@ const getAtlasBackups = (req, res) => {
               result = result.concat(obj2);
               res.send(result);
             })
-            .catch( (err) => {
+            .catch((err) => {
               res.status(500);
               res.render('error', {
                 message: 'Can\'t query backup file logs',
                 error: err
               });
             });
         })
-        .catch( (err) => {
+        .catch((err) => {
           res.status(500);
           res.render('error', {
             message: 'Can\'t query backup files',
             error: err
           });
         });
     })
-    .catch( (err) => {
+    .catch((err) => {
       res.status(400);
       res.render('error', {
         message: 'Can\'t find atlas',
@@ -136,12 +137,12 @@ const log = async (req, res) => {
 
       const result = await db.get('log').findOne(obj);
       let length = 0;
-      if(result) {
+      if (result) {
         length = parseFloat(result.value.length);
       }
       const sum = parseFloat(json.value.length) + length;
-      await db.get('log').update(obj, {$set:{
-        'value.length':sum,
+      await db.get('log').update(obj, {$set: {
+        'value.length': sum,
         date: (new Date()).toJSON()
       }}, {upsert: true});
       res.send({length: sum});
@@ -168,7 +169,7 @@ const log = async (req, res) => {
 
   db.get('mri').update({
     source: json.value.source,
-    'mri.atlas':{$elemMatch:{filename:json.value.atlas}}
+    'mri.atlas': {$elemMatch: {filename: json.value.atlas}}
   }, {
     $set: {
       'mri.atlas.$.modified': (new Date()).toJSON(),

controller/api/index.js

@@ -1,4 +1,5 @@
 const express = require('express');
+
 const controller = require('./api.controller');
 
 const router = new express.Router();

controller/atlasmakerServer/atlasmaker-linalg.js

@@ -2,31 +2,31 @@
 // Linear algebra
 //========================================================================================
 const mulMatVec = (m, v) => [
-  m[0][0]*v[0] + m[0][1]*v[1] + m[0][2]*v[2],
-  m[1][0]*v[0] + m[1][1]*v[1] + m[1][2]*v[2],
-  m[2][0]*v[0] + m[2][1]*v[1] + m[2][2]*v[2]
+  m[0][0] * v[0] + m[0][1] * v[1] + m[0][2] * v[2],
+  m[1][0] * v[0] + m[1][1] * v[1] + m[1][2] * v[2],
+  m[2][0] * v[0] + m[2][1] * v[1] + m[2][2] * v[2]
 ];
 
 const invMat = (m) => {
   const w = [[], [], []];
-  const det = m[0][1]*m[1][2]*m[2][0] + m[0][2]*m[1][0]*m[2][1] + m[0][0]*m[1][1]*m[2][2] - m[0][2]*m[1][1]*m[2][0] - m[0][0]*m[1][2]*m[2][1] - m[0][1]*m[1][0]*m[2][2];
+  const det = m[0][1] * m[1][2] * m[2][0] + m[0][2] * m[1][0] * m[2][1] + m[0][0] * m[1][1] * m[2][2] - m[0][2] * m[1][1] * m[2][0] - m[0][0] * m[1][2] * m[2][1] - m[0][1] * m[1][0] * m[2][2];
 
-  w[0][0] = (m[1][1]*m[2][2] - m[1][2]*m[2][1])/det;
-  w[0][1] = (m[0][2]*m[2][1] - m[0][1]*m[2][2])/det;
-  w[0][2] = (m[0][1]*m[1][2] - m[0][2]*m[1][1])/det;
+  w[0][0] = (m[1][1] * m[2][2] - m[1][2] * m[2][1]) / det;
+  w[0][1] = (m[0][2] * m[2][1] - m[0][1] * m[2][2]) / det;
+  w[0][2] = (m[0][1] * m[1][2] - m[0][2] * m[1][1]) / det;
 
-  w[1][0] = (m[1][2]*m[2][0] - m[1][0]*m[2][2])/det;
-  w[1][1] = (m[0][0]*m[2][2] - m[0][2]*m[2][0])/det;
-  w[1][2] = (m[0][2]*m[1][0] - m[0][0]*m[1][2])/det;
+  w[1][0] = (m[1][2] * m[2][0] - m[1][0] * m[2][2]) / det;
+  w[1][1] = (m[0][0] * m[2][2] - m[0][2] * m[2][0]) / det;
+  w[1][2] = (m[0][2] * m[1][0] - m[0][0] * m[1][2]) / det;
 
-  w[2][0] = (m[1][0]*m[2][1] - m[1][1]*m[2][0])/det;
-  w[2][1] = (m[0][1]*m[2][0] - m[0][0]*m[2][1])/det;
-  w[2][2] = (m[0][0]*m[1][1] - m[0][1]*m[1][0])/det;
+  w[2][0] = (m[1][0] * m[2][1] - m[1][1] * m[2][0]) / det;
+  w[2][1] = (m[0][1] * m[2][0] - m[0][0] * m[2][1]) / det;
+  w[2][2] = (m[0][0] * m[1][1] - m[0][1] * m[1][0]) / det;
 
   return w;
 };
 
-const subVecVec = (a, b) => [a[0]-b[0], a[1]-b[1], a[2]-b[2]];
+const subVecVec = (a, b) => [a[0] - b[0], a[1] - b[1], a[2] - b[2]];
 
 const addVecVec = (a, b) => [a[0] + b[0], a[1] + b[1], a[2] + b[2]];
 

controller/atlasmakerServer/atlasmaker-mri.js

@@ -4,9 +4,12 @@
 //========================================================================================
 
 const fs = require('fs');
-const Struct = require('struct');
-const zlib = require('zlib');
 const { promisify } = require('util');
+const zlib = require('zlib');
+
+const Struct = require('struct');
+
+
 const gunzip = promisify(zlib.gunzip);
 const la = require('./atlasmaker-linalg');
 
@@ -198,8 +201,7 @@ const computeS2VTransformation = (mri) => {
 const filetypeFromFilename = (mriPath) => {
   if (mriPath.match(/.nii.gz$/)) {
     return 'nii.gz';
-  } else
-  if (mriPath.match(/.mgz$/)) {
+  } else if (mriPath.match(/.mgz$/)) {
     return 'mgz';
   }
 };
@@ -646,8 +648,8 @@ const loadMRI = (mriPath) => {
         });
       break;
     default:
-      console.error('ERROR: nothing we can read');
-      reject(new Error('ERROR: nothing we can read'));
+      console.error('ERROR: nothing we can read ' + mriPath);
+      reject(new Error('ERROR: nothing we can read ' + mriPath));
     }
   });