[MAJOR] added CDATA to ARFF convertor, added Pipeline RIA visuals, mi…

…nor updates to RIA, removed unnecessary fetch files. [WIP] Mapping CLI API to the RIA

.babelrc

@@ -1,4 +1,4 @@
 {
   "presets": ["env", "react"],
-  "plugins": ["react-hot-loader/babel", "transform-object-rest-spread"]
+  "plugins": ["transform-object-rest-spread"]
 }

.gitignore

@@ -19,3 +19,4 @@ npm-debug.log
 CRES
 snippet
 .DS_Store
+.tmp_eset

Makefile

@@ -40,13 +40,13 @@ docs:
 	cd $(DOCSDIR) && make html
 
 kill:
-	fuser -k $(SERVER_PORT)/tcp
+	lsof -i TCP:$(SERVER_PORT) | grep LISTEN | awk '{print $2}' | xargs kill -9
 
 sass:
 	sass $(SOURCEDIR)/app/client/styles/App.scss:$(SOURCEDIR)/app/assets/css/styles.min.css --sourcemap=none --style compressed
 
 run:
-	$(PYTHON) -m $(PACKAGE) & npm start
+	npm start & $(PYTHON) -m $(PACKAGE)
 
 loc:
 	( find $(SOURCEDIR) -name "*.py"  -print0 | xargs -0 cat ) | wc -l

README.md

@@ -1,5 +1,5 @@
 <div align="center">
-  <img src=".github/logo-title.png" width="512">
+  <img src=".github/logo-w-title.png" width="512">
 </div>
 
 ---
@@ -27,6 +27,7 @@
 ### Table of Contents
 * [Installation](#installation)
 * [Usage](#usage)
+* [Features](#features)
 * [Dependencies](#dependencies)
 * [License](#license)
 
@@ -64,12 +65,32 @@ via Python
 >>> candis.main()
 ```
 
+**Using the CLI (Command Line Interface)**
+
+```
+$ candis --cdata path/to/data.cdata --config path/to/config.json
+```
+
+### Features
+* Converting a CDATA (with paths to DNA microarray files) to an **ARFF** file
+
+  ```python
+  >>> import candis
+  >>> cdata = candis.cdata.read('path/to/data.cdata')
+  ```
+
+  Then, simply use the `CData.toARFF` API:
+  ```python
+  >>> cdata.toARFF('path/to/data.arff')
+  ```
+
 ### Demo
 Check out a live demo of the application [here](https://cancerdiscover.herokuapp.com).
 
 ### Dependencies
 * Production Dependencies
   * R
+  * WEKA (***NOTE:*** Requires Java)
   * Python 2.7+ or Python 3.5+
 * Development Dependencies
   * [Node.js](https://nodejs.org)

TODO.md

@@ -1,5 +1,5 @@
 <div align="center">
-  <img src=".github/logo.png" width="512">
+  <img src=".github/logo-w-title.png" width="512">
 </div>
 
 ---
@@ -31,7 +31,6 @@
   * [ ] Documentation
 
 * #### Low Priority
-  * [x] Authentication Flow
   * [ ] Settings Dialog and Manager
   * [ ] Handling multiple tabs on Document Processor (Add Horizontal Scroll)
   * [ ] Random Forest Icon

candis/__init__.py

@@ -1,8 +1,8 @@
 # module - candis
-from candis.config  import Config, get_config, CONFIG
-from candis.manager import Cache
-from candis.ios     import cdata, pipeline
+from candis.config    import Config, get_config, CONFIG
+from candis.ios       import cdata, pipeline
+from candis.ios.cdata import CData
 # candis.cli
-from candis.cli     import main
+from candis.cli    import main
 
 __version__ = CONFIG.VERSION

candis/app/__init__.py

@@ -1,3 +1,3 @@
 # module - candis.app
 from candis.app.server import app
-from candis.app.main   import main
+from candis.app.main   import main