Merge branch 'master' into master

r03ert0 · Jun 13, 2020 · c7e3cb2 · c7e3cb2
2 parents 1c644fc + 7ee7571
commit c7e3cb2
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Showing 288 changed files with 5,099 additions and 108,663 deletions.
diff --git a/.eslintrc.js b/.eslintrc.js
@@ -71,7 +71,7 @@ module.exports = {
         "id-blacklist": "error",
         "id-length": "off",
         "id-match": "error",
-        "indent": "off",
+        "indent": ["error", 2],
         "indent-legacy": "off",
         "init-declarations": "off",
         "jsx-quotes": "error",

diff --git a/.gitignore b/.gitignore
@@ -21,3 +21,4 @@ test/*.png
 .vscode
 access.log
 package-lock.json
+app/controller/api/tmp
diff --git a/app/app.js b/app/app.js
@@ -11,32 +11,32 @@ const app = express();
 // uncomment after placing your favicon in /public
 //app.use(favicon(path.join(__dirname, 'public', 'favicon.ico')));
 if (process.env.NODE_ENV !== 'production') {
-    app.use(require('morgan')('dev'));
+  app.use(require('morgan')('dev'));
 }
 app.use(bodyParser.json());
 app.use(bodyParser.urlencoded({ extended: false }));
 app.use(express.static(path.join(__dirname, 'public')));
 
+
 /* setup DB */
 var checkAnyoneUser = function () {
 
-    /* check that the 'anyone' user exists. Insert it if it doesn't */
-    db.queryUser({username: 'anyone'})
+  /* check that the 'anyone' user exists. Insert it if it doesn't */
+  db.queryUser({username: 'anyone'})
     .then((res) => {
-        console.log('"anyone" user correctly configured.', res);
+      console.log('"anyone" user correctly configured.', res);
     })
     .catch((err) => {
-        console.log('"anyone" user absent: adding one.', err);
-        const anyone = {
-            username: 'anyone',
-            nickname: 'anyone',
-            name: 'Any User',
-            joined: (new Date()).toJSON()
-        };
-        db.addUser(anyone);
+      console.log('"anyone" user absent: adding one.', err);
+      const anyone = {
+        username: 'anyone',
+        nickname: 'anyone',
+        name: 'Any User',
+        joined: (new Date()).toJSON()
+      };
+      db.addUser(anyone);
     });
 };
-
 const db = require('./db/db')(null, checkAnyoneUser);
 app.db = db;
 
@@ -49,21 +49,21 @@ require('./routes/routes')(app);
 
 // catch 404 and forward to error handler
 app.use(function(req, res, next) {
-    console.log('ERROR: File not found', req.url);
-    var err = new Error('Not Found', req);
-    err.status = 404;
-    next(err);
+  console.log('ERROR: File not found', req.url);
+  var err = new Error('Not Found', req);
+  err.status = 404;
+  next(err);
 });
 
 // error handler
 app.use(function(err, req, res) {
-    // set locals, only providing error in development
-    res.locals.message = err.message;
-    res.locals.error = req.app.get('env') === 'development' ? err : {};
+  // set locals, only providing error in development
+  res.locals.message = err.message;
+  res.locals.error = req.app.get('env') === 'development' ? err : {};
 
-    // render the error page
-    res.status(err.status || 500);
-    res.render('error');
+  // render the error page
+  res.status(err.status || 500);
+  res.render('error');
 });
 
 

diff --git a/app/controller/api/api.spec.js b/app/controller/api/api.spec.js
@@ -12,8 +12,6 @@ const app = express()
 function buildFileID({source, slice}) {
     return `${source}&slice=${slice}`;
 }
-
-// app.use(bodyParser.urlencoded({ extended: false }))
 app.use(bodyParser.urlencoded({ extended: true }))
 
 /**
@@ -107,8 +105,7 @@ describe('controller/api/index.js', () => {
         returnFoundAnnotation = true,
         updateAnnotation = sinon.stub().resolves(), 
         findAnnotations = sinon.stub().callsFake(() => Promise.resolve( returnFoundAnnotation ? annoationInDb : {Regions: []} )),
-        queryProject = sinon.stub().callsFake(() => Promise.resolve(queryPublicProject ? publicProject : privateProject))
-
+        queryProject = sinon.stub().callsFake(() => Promise.resolve(queryPublicProject ? publicProject : privateProject))        
 
     before(() => {
         app.db = {

diff --git a/app/controller/api/index.js b/app/controller/api/index.js
@@ -26,22 +26,24 @@ router.get('/', async function (req, res) {
     const project = (req.query.project) || '';
     console.log(`current project: ${project}`);
 
-    // project owner and project users
-    const result = await req.app.db.queryProject({shortname: project});
-    const owner = result
-                  && result.owner;
-    const users = result
-                  && result.collaborators
-                  && result.collaborators.list
-                  && result.collaborators.list.map((u)=>u.username);
-    console.log(`project owner: ${owner}, users: ${users}`);
-
-    // check if user is among the allowed project's users
-    userIndex = [...users, owner].indexOf(user);
-    if(userIndex<0) {
-        res.status(403).send(`User ${user} not part of project ${project}`);
+    if(project) {
+        // project owner and project users
+        const result = await req.app.db.queryProject({shortname: project});
+        const owner = result
+                    && result.owner;
+        const users = result
+                    && result.collaborators
+                    && result.collaborators.list
+                    && result.collaborators.list.map((u)=>u.username) || [];
+        console.log(`project owner: ${owner}, users: ${users}`);
 
-        return;
+        // check if user is among the allowed project's users
+        userIndex = [...users, owner].indexOf(user);
+        if(userIndex<0) {
+            res.status(403).send(`User ${user} not part of project ${project}`);
+
+            return;
+        }
     }
 
     const query = {
@@ -51,7 +53,12 @@ router.get('/', async function (req, res) {
     };
     console.log("api get query", query);
 
-    const annotations = await req.app.db.findAnnotations(query);
+    let annotations;
+    try {
+      annotations = await req.app.db.findAnnotations(query);
+    } catch(err) {
+      throw new Error(err);
+    }
 
     res.status(200).send(annotations);
 });
@@ -72,21 +79,23 @@ const saveFromGUI = async function (req, res) {
     console.log(`current project: ${project}`);
 
     // project owner and project users
-    const result = await req.app.db.queryProject({shortname: project});
-    const owner = result
-                    && result.owner;
-    const users = result
-                    && result.collaborators
-                    && result.collaborators.list
-                    && result.collaborators.list.map((u)=>u.username);
-    console.log(`project owner: ${owner}, users: ${users}`);
-
-    // check if user is among the allowed project's users
-    userIndex = [...users, owner].indexOf(user);
-    if(userIndex<0) {
+    if(project) {
+      const result = await req.app.db.queryProject({shortname: project});
+      const owner = result
+        && result.owner;
+      const users = result
+        && result.collaborators
+        && result.collaborators.list
+        && result.collaborators.list.map((u)=>u.username);
+      console.log(`project owner: ${owner}, users: ${users}`);
+
+      // check if user is among the allowed project's users
+      userIndex = [...users, owner].indexOf(user);
+      if(userIndex<0) {
         res.status(403).send(`User ${user} not part of project ${project}`);
 
         return;
+      }
     }
 
     req.app.db.updateAnnotation({
@@ -96,8 +105,8 @@ const saveFromGUI = async function (req, res) {
         Hash,
         annotation
     })
-        .then(() => res.status(200).send())
-        .catch((e) => res.status(500).send({err:JSON.stringify(e)}));
+    .then(() => res.status(200).send())
+    .catch((e) => res.status(500).send({err:JSON.stringify(e)}));
 };
 
 /**

diff --git a/app/db/db.js b/app/db/db.js
@@ -28,9 +28,9 @@ module.exports = function(overwriteMongoPath, callback) {
             return reject(new Error('db connection not healthy'));
         }
         db.get('user').update({
-            username : user.username
+            username: user.username
         }, {
-            $set : user
+            $set: user
         })
         .then(() => resolve(user))
         .catch(reject);
@@ -189,13 +189,12 @@ module.exports = function(overwriteMongoPath, callback) {
         if (!checkHealth()) {
             return reject(new Error('db connection not healthy'));
         }
-        console.log('updateProject:', project);
+        delete project._id;
         db.get('projects').update(
-            { shortname : project.shortname },
-            project
+            { shortname: project.shortname },
+            { $set: project }
         )
             .then((o) => {
-                console.log('updateProject', o);
                 resolve(o);
             })
             .catch(reject);
@@ -245,37 +244,37 @@ module.exports = function(overwriteMongoPath, callback) {
             return reject(new Error('db connection not healthy'));
         }
         db.get('projects').find(pagination)
-            .then((projects) => {
-                if(projects) {
-                    resolve(projects);
-                } else {
-                    reject({message: 'error find all projects', result: projects});
-                }
-            })
-            .catch((e) => reject(e));
+          .then((projects) => {
+            if(projects) {
+              resolve(projects);
+            } else {
+              reject({message: 'error find all projects', result: projects});
+            }
+          })
+          .catch((e) => reject(e));
     });
 
     /* query user projects */
     const queryUserProjects = (requestedUser) => new Promise((resolve, reject) => {
-        if (!checkHealth()) {
-            return reject(new Error('db connection not healthy'));
-        }
-        db.get('projects').find({
-            $or: [
-                {owner: requestedUser},
-                {"collaborators.list": {$elemMatch:{userID: requestedUser}}}
-            ],
-            backup: {$exists: false}
+      if (!checkHealth()) {
+          return reject(new Error('db connection not healthy'));
+      }
+      db.get('projects').find({
+        $or: [
+          {owner: requestedUser},
+          {"collaborators.list": {$elemMatch:{userID: requestedUser}}}
+        ],
+        backup: {$exists: false}
+      })
+        // @todo the results should be access filtered
+        .then((projects) => {
+          if(projects) {
+              resolve(projects);
+          } else {
+            reject({message: 'error find all projects', result: projects});
+          }
         })
-            // @todo the results should be access filtered
-            .then((projects) => {
-                if(projects) {
-                    resolve(projects);
-                } else {
-                    reject({message: 'error find all projects', result: projects});
-                }
-            })
-            .catch(reject);
+        .catch(reject);
     });
 
     /* search users */
@@ -303,21 +302,20 @@ module.exports = function(overwriteMongoPath, callback) {
             .catch(reject);
     });
 
-    db
-        .then(() => {
-            connected = true;
+    db.then(() => {
+      connected = true;
 
-            console.log('connected successfully');
+      console.log('connected successfully');
 
-            if(typeof callback !== 'undefined') {
-                return callback();
-            }
-        })
-        .catch((e) => {
-            // retry (?)
-            connected = false;
-            console.log('connection error', e);
-        });
+      if(typeof callback !== 'undefined') {
+          return callback();
+      }
+    })
+    .catch((e) => {
+      // retry (?)
+      connected = false;
+      console.log('connection error', e);
+    });
 
     return {
         addUser,

diff --git a/app/public/css/data-style.css b/app/public/css/data-style.css
@@ -1,11 +1,3 @@
-html,body {
-    margin:0px;
-    background-color: #333;
-}
-* {
-    font-family: sans-serif;
-    font-size:1rem;
-}
 #header {
     height:48px;
 }
@@ -27,10 +19,8 @@ html,body {
     font-weight: lighter;
 }
 #menu {
-    float:right;
     margin-right: 10px;
     display: inline-block;
-    font: 16px/24px "Lucida Grande", "Lucida Sans Unicode", Helvetica, Arial, Verdana, sans-serif;
 }
 #MyLogin {
      display:inline-block;
@@ -56,22 +46,6 @@ html,body {
     z-index:1;
 }
 
-#paperjs-container
-{
-    width:100%;
-    height:100%;
-    position:absolute;
-    top:0;
-    left:0;
-    z-index:2;
-    pointer-events: none;
-}
-
-#paperjs-container canvas
-{
-    /* pointer-events:  */
-}
-
 #colorSelector,
 #colorSelector *
 {

diff --git a/app/public/css/index-style.css b/app/public/css/index-style.css
@@ -1,5 +1,5 @@
 html, #menu, #footer {
-    background-color: #111;
+    background-color: #222;
 }
 #footer {
     display: block;
@@ -27,7 +27,6 @@ html, #menu, #footer {
     margin-top:0;
     width: 100%;
     display: inline-block;
-    font: 16px/24px "Lucida Grande", "Lucida Sans Unicode", Helvetica, Arial, Verdana, sans-serif;
     transition: top .5s, opacity .5s;
     -moz-transition: top .5s, opacity .5s;
     -webkit-transition: top .5s, opacity .5s;