Merge pull request #28 from neuroanatomy/master

sync fork

Author: r03ert0

.gitignore

@@ -5,6 +5,7 @@ admin
 blacklist.json
 bulk-upload.sh
 github-keys.json
+js/.DS_Store
 node_modules
 npm-debug.log
 public/.DS_Store
@@ -20,10 +21,11 @@ public/lib/.DS_Store
 public/lib/atlasMaker.js
 public/lib/atlasMaker-tools
 public/lib/brainbox.js
+scripts/atlasMaker-resources.js
 test/screenshots/
 tmp
 view/atlasMaker/dist/
 view/atlasMaker/src/tools/dist/
 view/brainbox/dist/
 whitelist.json
-js/.DS_Store
+ws_cfg.json

ANNOTATIONS.md

@@ -1,5 +1,5 @@
 **Come and join our team of
- [BrainMappers](https://github.com/OpenNeuroLab/BrainBox/blob/master/BRAINMAPPERS.md)!!**  
+ [BrainMappers](https://github.com/neuroanatomy/BrainBox/blob/master/BRAINMAPPERS.md)!!**
 We will be happy to work with anyone who would love to join our effort.
  While you can see in real-time what your collaborators are writing or drawing on a given
  data set, you can also chat with them, and ask for help or approval of your work. We want
@@ -14,8 +14,8 @@ Come to our [**dolphin brain**](http://brainbox.pasteur.fr/mri?url=http://brainc
 
 <img width="769" alt="screen shot 2017-06-01 at 11 08 34" src="https://cloud.githubusercontent.com/assets/6297454/26672835/f7892d80-46ba-11e7-8be8-51adbee9288d.png">
 
-When you have done 1 slice, 
-* add your name or github handle to our [BRAINMAPPERS.md](https://github.com/OpenNeuroLab/BrainBox/blob/master/BRAINMAPPERS.md) file
+When you have done 1 slice,
+* add your name or github handle to our [BRAINMAPPERS.md](https://github.com/neuroanatomy/BrainBox/blob/master/BRAINMAPPERS.md) file
 * add the slice number where you have been working (currently, 111 & 112 are done, you could continue with 113++)
 * add "length:..." and 
 * "volume:..." from the upper left corner of the BrainBox viewer into the file (just for the fun!! :D)

BRAINMAPPERS.md

@@ -1,12 +1,14 @@
 :sparkles: We are the brain mappers! \ö/ :sparkles:
 
-Here, we are segmenting an amazingly folded [**dolphin brain**](http://brainbox.pasteur.fr/mri?url=http://braincatalogue.org/data/Bottlenose_dolphin/MRI-n4.nii.gz&view=cor&slice=143). Once you clicked the link, you will find our work in progress on the dolphin brain in the Braincatalogue project. You can **join our segmentation sprint any time!** You can also choose a different species to work on, if you prefer! Any contributions are featured below. More information on segmenting can be found in our [ANNOTATIONS.md file](https://github.com/OpenNeuroLab/BrainBox/blob/master/ANNOTATIONS.md).
+Here, we are segmenting an amazingly folded [**dolphin brain**](http://brainbox.pasteur.fr/mri?url=http://braincatalogue.org/data/Bottlenose_dolphin/MRI-n4.nii.gz&view=cor&slice=143). Once you clicked the link, you will find our work in progress on the dolphin brain in the Braincatalogue project. You can **join our segmentation sprint any time!** You can also choose a different species to work on, if you prefer! Any contributions are featured below. More information on segmenting can be found in our [ANNOTATIONS.md file](https://github.com/neuroanatomy/BrainBox/blob/master/ANNOTATIONS.md).
 
 <img width="769" alt="screen shot 2017-06-01 at 11 08 34" src="https://cloud.githubusercontent.com/assets/6297454/26672835/f7892d80-46ba-11e7-8be8-51adbee9288d.png">
 
 **Our BrainMapper team**
 
-current Volume segmented: **509 368 mm3** (please update! :D)
+initial volume segmented: 509 368 mm3
+
+current volume segmented: **445 823 mm3** (please update! :D)
 
 Name:               **name**  
 GitHub:             @  
@@ -15,6 +17,12 @@ Slice numbers:      axial (cor) __
 Length:             __ mm  
 Volume:             __ mm3  
 
+Name:               **faruk**  
+GitHub:             @ofgulban  
+Species:            Bottlenose dolphin  
+Slice numbers:      all  
+Length:             mm  
+Volume:             445 823 mm3  
 
 Name:               **katja**  
 GitHub:             @katjaq  

CONTRIBUTING.md

@@ -4,10 +4,10 @@
 
 
 **Join our segmentation sprints!**
- In our [GitHub issue #42](https://github.com/OpenNeuroLab/BrainBox/issues/177) you find
+ In our [GitHub issue #42](https://github.com/neuroanatomy/BrainBox/issues/177) you find
  detailed information on how to participate and get credit for your work. Currently, we
  are trying to complete the dolphin brain!! Join our team of
- [BrainMappers](https://github.com/OpenNeuroLab/BrainBox/blob/master/BRAINMAPPERS.md)
+ [BrainMappers](https://github.com/neuroanatomy/BrainBox/blob/master/BRAINMAPPERS.md)
  We will be happy to work with anyone who would love to join our effort.
  While you can see in real-time what your collaborators are writing or drawing on a given
  data set, you can also chat with them, and ask for help or approval of your work. We want

README.md

@@ -34,7 +34,7 @@ Our aim is to make BrainBox into a reliable tool for open, reproducible, collabo
 
 We will be happy to work with anyone who would love to join our effort.
 While you can see in real-time what your collaborators are writing or drawing on a given data set, you can also chat with them, and ask for help or approval of your work. We want to open this scientific process to everyone with any background including citizen scientists and researchers. Join us!
-**Join our segmentation sprint!** In our [GitHub issue #42](https://github.com/OpenNeuroLab/BrainBox/issues/177) you find detailed information on how to participate and get credit for your work. Currently, we are trying to complete the dolphin brain! Join our team of [BrainMappers](https://github.com/OpenNeuroLab/BrainBox/blob/master/BRAINMAPPERS.md)
+**Join our segmentation sprint!** In our [GitHub issue #42](https://github.com/neuroanatomy/BrainBox/issues/177) you find detailed information on how to participate and get credit for your work. Currently, we are trying to complete the dolphin brain! Join our team of [BrainMappers](https://github.com/neuroanatomy/BrainBox/blob/master/BRAINMAPPERS.md)
 
 And please also feel free to join our efforts on GitHub! Everybody very welcome!
 

app.js

@@ -36,7 +36,6 @@ if (DOCKER_DB) {
 }
 
 var db = monk(MONGO_DB);
-var fs = require('fs');
 var expressValidator = require('express-validator');
 
 /* jslint nomen: true */
@@ -197,7 +196,7 @@ app.get('/auth/github/callback',
 global.tokenAuthentication = function (req, res, next) {
     tracer.log('>> Check token');
     let token;
-    if (req.params.token) {
+    if (req.params.token)
         token = req.params.token;
     if(req.query.token)
         token = req.query.token;

controller/project/project.controller.js

@@ -1,9 +1,3 @@
-var async = require("async");
-var url = require('url');
-var crypto = require('crypto');
-var dateFormat = require('dateformat');
-var validatorNPM = require('validator');
-var async = require('async');
 const url = require('url');
 const crypto = require('crypto');
 const dateFormat = require('dateformat');
@@ -52,7 +46,8 @@ var isProjectObject = function(req,res,object) {
 
     var pr = new Promise(function(resolve, reject) {
         var i, k, flag, arr;
-        var allowed="abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ01234567890.,_- '–:;".split("");
+        var allowed="abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789.,_- '–:;".split("");
+        var allowedAlphanumericHyphen="abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789-".split("");
 
         // 1. Synchronous checks
         //----------------------
@@ -96,7 +91,7 @@ var isProjectObject = function(req,res,object) {
         console.log("> owner and project shortname present")
 
         // check that shortname is alphanumeric
-        if(!validatorNPM.isAlphanumeric(object.owner) || !validatorNPM.isAlphanumeric(object.shortname)) {
+        if(!validatorNPM.isWhitelisted(object.owner, allowedAlphanumericHyphen) || !validatorNPM.isWhitelisted(object.shortname, allowedAlphanumericHyphen)) {
             reject({success:false,error:"Invalid owner or project shortname, not alphanumeric"});
             return;
         }