Blackbird

README.md

@@ -41,6 +41,8 @@ JSZip: http://stuk.github.io/jszip/<br>
 Lo-Dash: http://lodash.com/<br>
 lz-string: https://github.com/pieroxy/lz-string<br>
 md5-js: https://github.com/wbond/md5-js<br>
+biom-conversion-server: https://github.com/molbiodiv/biom-conversion-server<br>
+biojs-io-biom: https://github.com/molbiodiv/biojs-io-biom<br>
 
 ## License
 The BSD 2-Clause License

data/dbschema.sql

@@ -67,6 +67,7 @@ CREATE TABLE IF NOT EXISTS `SharedData` (
   `visualization_options` text NOT NULL,
   `date_uploaded` datetime NOT NULL,
   `countView` int(10) NOT NULL,
+  `filter_options_json` text NOT NULL,
   PRIMARY KEY (`SharedData_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 AUTO_INCREMENT=1 ;
 

index.html

@@ -13,6 +13,7 @@
     <meta property="og:image" content="img/phinch-logo.jpg">
     <meta property="og:site_name" content="PHINCH">
 
+	<script src="lib/jquery-1.10.1.min.js"></script>
     <!-- Google Analytics -->
 	<script type="text/javascript">
 		var _gaq = _gaq || [];
@@ -130,12 +131,12 @@ <h1>About Phinch</h1>
 		Copyright © 2014 Phinch. Phinch is supported by the <a href="http://www.sloan.org/" target="_blank">Alfred P. Sloan Foundation</a>. This content is released under <a href="http://opensource.org/licenses/BSD-2-Clause" target="_blank">The BSD 2-Clause License</a>. <span><a href="https://groups.google.com/forum/#!forum/phinch" target="_blank"><i class="icon-fa-users icon-large"></i>&nbsp;&nbsp;Google Group</a>&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://github.com/PitchInteractiveInc/Phinch" target="_blank"><i class="icon-github icon-large"></i>&nbsp;&nbsp;Github</a></span>
 	</section>
 
+	<script src="lib/biojs-io-biom.min.js"></script>
 	<script src="lib/indexedDB.polyfill.js"></script>
 	<script src="lib/db.js"></script>
-	<script src="lib/jquery-1.10.1.min.js"></script>
 	<script src="lib/jquery-ui-1.10.3.custom.min.js"></script>
 	<script src="lib/blob.js"></script>
-	
+
 	<script src="scripts/readFile.js"></script>
 	<script src="scripts/init.js"></script>
     <script> var app; window.onload = function() { app = new init('home');} </script>

server/composer.json

@@ -0,0 +1,5 @@
+{
+    "require": {
+        "iimog/biom-conversion-server": "^1.0"
+    }
+}

server/convert.php

@@ -0,0 +1,63 @@
+<?php
+
+namespace biomcs;
+
+/**
+ * This file converts base64 encoded "content" "to" the desired format (hdf5 or json)
+ * The output format is json that contains biom data base64 encoded as part of the output array:
+ * Example:
+ * {
+ *   content: "iUhERg0KGgoAAAAAAAgIAAQAEAAAAAAAAAAAAAAAAAD\/\/\/\/\/\/\/\/\/\/zCEAAAAAAAA...AAAAAAAAAAAAAAAAAAA",
+ *   error: null
+ * }
+ */
+
+// Allow CORS
+header("Access-Control-Allow-Origin: *");
+header("Access-Control-Allow-Headers: Content-Type");
+// Set own content type
+header("Content-Type: application/json");
+
+require_once __DIR__ . DIRECTORY_SEPARATOR . 'vendor' . DIRECTORY_SEPARATOR . 'autoload.php';
+// explicitly set CONTENT_TYPE if empty (required for testing)
+if(empty($_SERVER['CONTENT_TYPE']))
+{
+    $_SERVER['CONTENT_TYPE'] = "application/x-www-form-urlencoded";
+}
+// load json data into $_REQUEST if content type is application/json
+if($_SERVER["CONTENT_TYPE"] === 'application/json'){
+    $_REQUEST = json_decode(file_get_contents('php://input'), true);
+}
+$to = isset($_REQUEST["to"]) ? $_REQUEST["to"] : false;
+$content = isset($_REQUEST["content"]) ? $_REQUEST["content"] : false;
+$content = base64_decode($content);
+if (!$to) {
+    echo json_encode(array("error" => "Missing parameter 'to' please set to 'json' or 'hdf5'"));
+} elseif ($to !== 'json' && $to !== 'hdf5') {
+    echo json_encode(array("error" => "Illegal value of 'to' parameter please set to 'json' or 'hdf5'"));
+} elseif (!$content) {
+    echo json_encode(array("error" => "Missing parameter 'content' please send the content to convert as base64 encoded string"));
+} else {
+    $biomcs = new BiomCS();
+    try {
+        if ($to === "json") {
+            echo json_encode(
+                array(
+                    "content" => base64_encode($biomcs->convertToJSON($content)),
+                    "error" => null
+                ),
+                JSON_PRETTY_PRINT
+            );
+        } elseif ($to === "hdf5") {
+            print json_encode(
+                array(
+                    "content" => base64_encode($biomcs->convertToHDF5($content)),
+                    "error" => null
+                ),
+                JSON_PRETTY_PRINT
+            );
+        }
+    } catch (\Exception $e) {
+        echo json_encode(array("error" => $e->getMessage()), JSON_PRETTY_PRINT);
+    }
+}

server/dbconfig-sample.php

@@ -7,7 +7,6 @@
 );
 
 
-$db = new PDO('mysql:host=' . $dbConfig['host'].';dbname=' . $dbConfig['host'],
+$db = new PDO('mysql:host=' . $dbConfig['host'].';dbname=' . $dbConfig['dbname'],
  $dbConfig['username'], $dbConfig['password']);
-var_dump($db)
 ?>

server/vendor/autoload.php

@@ -0,0 +1,7 @@
+<?php
+
+// autoload.php @generated by Composer
+
+require_once __DIR__ . '/composer' . '/autoload_real.php';
+
+return ComposerAutoloaderInit2098943a8ff25d68413e17489441d42a::getLoader();