Merge pull request #29 from neuroanatomy/master

big update

Author: r03ert0

.eslintrc.js

@@ -6,7 +6,8 @@ module.exports = {
     },
     "extends": "eslint:recommended",
     "parserOptions": {
-        "sourceType": "module"
+        "sourceType": "module",
+        "ecmaVersion": 8
     },
     "rules": {
         "accessor-pairs": "error",
@@ -89,7 +90,7 @@ module.exports = {
         "max-lines": "error",
         "max-nested-callbacks": "error",
         "max-params": "off",
-        "max-statements": "error",
+        "max-statements": ["error", 100],
         "max-statements-per-line": "off",
         "multiline-ternary": [
             "error",

ANNOTATIONS.md

@@ -7,7 +7,7 @@
  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)
+ [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

BRAINMAPPERS.md

@@ -0,0 +1,25 @@
+## Thank you for your feedback.
+
+### Please tag your issue as a feature request or a bug report using the labels on the right. 
+
+### Current behaviour
+
+* If this is a bug, please explain how to reproduce the problem 
+    * Which tools did you use in which sequence?
+    * Is the error concerning a text or a volume annotation? 
+    * Which label set has been used for the volume annotation (if applicable)?
+    * What is the type and resolution of your data? (Can you provide a link to your data?)
+    * Do not include sensitive information.
+    * Upload the browser error message if you are familiar with web developer tools.
+
+### Expected behaviour
+
+### Version information (for bug reports)
+
+* **Browser + version**:
+* **Your OS + version**:
+* Paste the output of these commands:
+```
+node --version && npm --version
+```
+

CONTRIBUTING.md renamed to Contributing.md

@@ -1,4 +1,4 @@
-Copyright [2016] OpenNeuroLab Developers
+Copyright [2016] BrainBox Developers
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

Issue_Template.md

@@ -0,0 +1,79 @@
+<!-- Thank you for your contribution to BrainBox -->
+
+<!-- Give a short title and description for your pull request: -->
+
+---
+<!-- Run the tests. Replace each `[ ]` by `[X]` when the step is complete.-->
+- [ ] These changes fix #__ (github issue number if applicable).
+- [ ] ```npm run mocha-test``` ran with full success.
+- [ ] ```npm run mocha-test``` ran resulted in  failure in _____
+
+<!-- Replace `__` with appropriate information: -->
+- [ ] I implemented tests for the changes I made OR
+- [ ] These changes do not require tests because _____
+
+<!-- Make sure that "Allow edits from maintainers" checkbox is checked.-->
+
+<!-- Pull requests that do not address these steps are welcome, but they will require additional verification. -->
+
+
+- [ ] All BrainBox tools behave as expected:
+    * **KEYS**
+        * right and left arrow keys
+            - [ ] jump to next or previous slice within one brain, respectively
+            - [ ] update the slider accordingly
+            - [ ] update the slice number accordingly (upper left corner of the viewer window)
+        * down and up arrow keys
+            - [ ] jump to the next or previous brain within one project, respectively
+            - [ ] update the selected subject in the annotation table
+    * **TOOL BUTTONS**
+        * minus
+            - [ ] jumps to the previous slice within one brain
+            - [ ] updates the slider accordingly
+            - [ ] updates the slice number accordingly (upper left corner of the viewer window)
+        * plus
+            - [ ] jumps to the next slice within one brain
+            - [ ] updates the slider accordingly
+            - [ ] updates the slice number accordingly (upper left corner of the viewer window)
+        * slider
+            - [ ] updates slice view and slice number on the fly
+        * sag / cor / axi buttons
+            - [ ] switch view between the three orthogonal planes
+        * show tool
+            - [ ] when you click and drag in your browser window, this tool displays a cirlce at the position of your mouse click & drag as well as the user name in all browser windows connected to the same brain
+        * the numbers at the bottom of the tool panel
+            - [ ] change pencil size and eraser size accordingly
+        * pencil tool
+            - [ ] draws a line in the colour displayed in the color field
+            - [ ] in combination with bucket tool filles a complete area with the chosen colour (be sure to have closed the contour line ;) Otherwise, the undo button will be your friend ;)
+            - [ ] updates length and volume information (of what has been segmented) in the upper left corner of the viewer
+        * erase tool
+            - [ ] erases upon click drag from the annotation
+            - [ ] in combination with the bucket tool erases the complete area of the color where you click
+        * fill bucket tool
+            * in combination with pencil tool
+                - [ ] fills a complete area with the colour displayed in the colour field
+            * in combination with erase tool
+                - [ ] erases the complete area that is filled by the colour of where you click
+        * colour field
+            - [ ] displays the currently chosen colour to draw and fill
+            - [ ] on click opens the set of colours available within the chosen label set where a new colour can be selected upon click
+        * ruler tool
+            - [ ] measures the distance between start and end of your defined path
+                - [ ] points of mouse click appear and stay visible until you hit return key (this functionality is currently broken!) (you can click as many points as you wish to define the path you are interested in)
+                - [ ] on return key, BrainBox will print the distance into the chat field (the ruler tool seems to be currently broken!!!)
+        * adjust tool
+            - [ ] slide opacity of overlaid annotation from 0 to 100%
+            - [ ] increase or decrease brightness of the underlying MRI data
+            - [ ] increase or decrease the contrast of the underlying MRI data
+        * eyedropper tool
+            - [ ] updates the colour field in the tool panel
+            - [ ] displays/updates the region name in the upper left corner of the viewer
+        * undo tool
+            - [ ] undoes the user's actions in reverse chronological order and currently has the bug that it even undoes actions in slices you are currently not seeing! and there is currently no redo...
+        * save button
+            - [ ] saves the annotation of the data set into the data base
+            - [ ] displays a message that user needs to login in case they are not
+            - [ ] display a message `Atlas saved Wed Oct 18 2017 12:49:12 GMT+0200 (CEST)`
+
+

LICENSE

@@ -1,11 +1,11 @@
 
 [![CircleCI](https://circleci.com/gh/neuroanatomy/BrainBox/tree/master.svg?style=shield)](https://circleci.com/gh/neuroanatomy/BrainBox/tree/master) [![Join the chat at https://gitter.im/OpenNeuroLab-Brainbox/Lobby](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/OpenNeuroLab-Brainbox/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
-# BrainBox - An application from the [Open Neuroimaging Laboratory](http://openneu.ro/)
+# BrainBox - A platform for real-time collaboration in neuroimaging
 
 [![Join the chat at https://gitter.im/OpenNeuroLab-Brainbox/Lobby](https://badges.gitter.im/OpenNeuroLab-Brainbox/Lobby.svg)](https://gitter.im/OpenNeuroLab-Brainbox/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
-BrainBox is a web application for the collaborative curation of neuroimaging data
+BrainBox is a Web application for the collaborative curation of neuroimaging data
  available online. You can share, visualise and annotate MRI brain
  data in real-time, collaboratively. BrainBox will provide the means to create a
  layer of collaborative annotation over all the available MRI data without
@@ -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/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)
+**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!
 
@@ -68,7 +68,26 @@ Or launch your own collaborative project on [BrainBox](http://brainbox.pasteur.f
 
 If you want to work on BrainBox's code, you'll need a local installation:
 
+
+## Non docker developer install instructions
+
+1. install and start `mongo` database
+2. clone the repo and `cd` to the brainbox directory
+4. [create a new OAuth application](https://github.com/settings/applications/new) for your local brainbox url (http://localhost:3000 by default)
+5. paste the keys into the github-keys.json.example file, and drop the .example
+6. drop the `.example` from `controller/atlasMakerServer/blacklist.json.example`
+7. drop the `.example` from `controller/atlasMakerServer/whitelist.json.example`
+8. drop the `.example` from `blacklist.json.example`
+9. drop the `.example` from `whitelist.json.example`
+10. `npm install`
+11. `npm run prepare`
+12. `npm run build`
+13. `npm start`
+14. To check that your code style is like the one we use,  enter `npm run lint`, or you can type `eslint` before committing, to do that install `eslint` globally using `npm i -g eslint` (our code style rules are in the file `.eslintrc`).
+
+
 ## Using Docker to install and run BrainBox
+These installation instructions may need to be updated.  
 
 1. `git clone` this repository or download it
 2. `mv BrainBox brainbox` to rename the directory
@@ -81,17 +100,6 @@ If you want to work on BrainBox's code, you'll need a local installation:
 8. `docker-compose up`
 9. Then open `http://localhost:3000` in your browser.
 
-## Non docker developer install instructions
-
-1. install and start `mongo` database
-2. clone the repo and `cd` to the brainbox directory
-4. [create a new OAuth application](https://github.com/settings/applications/new) for your local brainbox url (http://localhost:3000 by default)
-5. paste the keys into the github-keys.json.example file, and drop the .example
-6. drop the `.example` from `controller/atlasMakerServer/blacklist.json.example`
-7. drop the `.example` from `controller/atlasMakerServer/whitelist.json.example`
-8. `npm install`
-9. `npm start`
-10. To check that your code style is like the one we use,  enter `npm run lint`, or you can type `eslint` before committing, to do that install `eslint` globally using `npm i -g eslint` (our code style rules are in the file `.eslintrc`).
 
 ## Tests