Multiple Organism Support Feature

Docker OpenPIP package/README.md

@@ -1,28 +1,47 @@
 
-# compose_PIP : INSTALLATION GUIDE FOR OPEN-PIP
---------packager for openPIP---------
+# INSTALLATION GUIDE FOR OPEN-PIP : composePIP 
+## Packager for openPIP
 
-Required and tested on:
+Required and tested on: *@ Docker version 20.10.7 and docker-compose version 1.29.2*
 
-***@** Docker version 20.10.7*
+## STEPS:
 
-***&** docker-compose version 1.29.2*
+***Prerequisites***
+<br>
+**STEP 1:** Install Docker Engine <br>
+*Reference:* https://docs.docker.com/engine/install/ubuntu/ <br>
+**STEP 2:** Install Docker compose <br>
+*Reference:* https://docs.docker.com/compose/install/ <br>
 
 
------------ STEPS -------------------
+***Source Code***
+<br>
+**STEP 3:** Clone OpenPIP repo from GitHub <br>
+>git clone https://github.com/BaderLab/openPIP.git 
+
+**STEP 4:** Inside OpenPIP folder run script `start.sh` <br>
+>chmod 777 ./start.sh && ./start.sh
 
-***Prerequisites* <br>**
-STEP 1: Install Docker Engine <br>
-*Reference:* https://docs.docker.com/engine/install/ubuntu/ <br>
-STEP 2: Install Docker compose <br>
-*Reference:* https://docs.docker.com/compose/install/ <br>
 <br>
-STEP 3: Clone OpenPIP repo from GitHub <br>
-```git clone https://github.com/aniket328/openPIP.git``` <br>
-and switch to branch `dev10.0`
+
+Hurray! :tada: :tada: The server is now running on <br>  
+
+:rocket: [localhost:80](http://localhost:80/app.php)  :rocket: 
+
+<br><br>
+
+<br><br>
+<br><br>
+<br><br>
+<br><br>
+
+
 
 
-STEP 4: 
+## TROUBLESHOOTING:
+
+
+START.SH: 
 
   1. get superuser access: ```sudo su```
   2. run this command inside openPIP folder:
@@ -33,7 +52,7 @@ STEP 4:
  (this may take few minutes)
  <br>
 
-STEP 5: populate database with `admin_settings` and `users` to establish connection.
+START.SH: populate database with `admin_settings` and `users` to establish connection.
 
 
     1. Exec into mysql container running:
@@ -47,12 +66,6 @@ STEP 5: populate database with `admin_settings` and `users` to establish connect
     3. RUN Command: 
         `source /db/init_new.sql`
 
-<br>
-Hurray! The server is now running on localhost:80
-<br><br>
-<br><br>
-
------------ ERRORS and Solutions -------------
 
 
 
@@ -87,5 +100,5 @@ Run:
     make sure you have replaced '\' in path with '/', in ubuntu.
 
 
---------
+-------- 
 

app/Resources/views/data_manager.html.twig

@@ -55,6 +55,89 @@
 
 <div class="container">
 	<div class="col-lg-10">
+		<div class="row">
+			<div class="col-lg-8" style="padding: 0px 0px;">
+				<div class="container data_upload_panel">
+					<div class="row">
+						<div class="data_upload_header" style="background-color: {{ main_color_scheme }}" >
+							<h4 style="color: {{ header_color_scheme }}">Add Organism</h4>
+						</div>
+					</div>
+
+					<div class="row data_upload_content" >
+						<div class="col-lg-12">		
+
+							<form action={{ path('admin_createOrganism') }} >
+								<div class="form-group">
+									<label for="organism_name">Name</label>
+									<input type="text" class="form-control" name="organism_name" id="organism_name" aria-describedby="Organism_Help" placeholder="Enter Organism Name" required>
+									<small id="emailHelp" class="form-text text-muted">A new organism will be created with this name.</small>
+								</div>
+								<div class="form-group">
+									<label for="organism_name">Taxonomy ID (optional)</label>
+									<input type="text" class="form-control" name="tax_id" id="tax_id" aria-describedby="Taxid_Help" placeholder="Enter Taxonomy ID">
+								</div>
+								<div class="form-group">
+									<label for="organism_name">Class (optional)</label>
+									<input type="text" class="form-control" name="organism_class" id="organism_class" aria-describedby="Class_Help" placeholder="Enter Organism Class">
+								</div>
+								<div class="form-group">
+									<label for="organism_name">Scientific Name (optional)</label>
+									<input type="text" class="form-control" name="scientific_name" id="scientific_name" aria-describedby="Scientific_Help" placeholder="Enter Scientific Name">
+								</div>
+								<div class="form-group">
+									<label for="organism_name">Description (optional)</label>
+									<input type="text" class="form-control" name="organism_description" id="organism_description" aria-describedby="organism_description" placeholder="Enter Description">
+								</div>
+								<button type="submit" class="btn btn-success">Create</button>
+							</form>					
+
+						</div>
+					</div>
+				</div>
+
+			</div>		
+
+			<div class="col-lg-4" style="padding: 0px 0px;">
+				<div class="container data_upload_panel">
+					<div class="row">
+						<div class="data_upload_header" style="background-color: {{ main_color_scheme }}">
+							<h4 style="color: {{ header_color_scheme }}">Delete Organism</h4>
+						</div>
+					</div>
+
+						{{form_start(organism_form)}}
+						{{form_end(organism_form)}}
+					<div class="row">
+						<button id="delete_dataset_button" class="btn btn-danger" style="margin: 20px;">
+							<i class="glyphicon glyphicon-ban-circle"></i> <span>Delete Organism</span>
+						</button>
+					</div>
+				</div>
+				<div class="container data_upload_panel">
+
+				</div>	
+				{# <form action="{{ path('upload_media', { 'dir_name': 'FASTA'}) }}" method="post" enctype="multipart/form-data">	
+					<input name="file" type="file" multiple />
+					<button type="submit" value="Submit">Submit</button>
+				</form>
+				<form method="post" id="sample_form" enctype="multipart/form-data">
+					<div class="form-group">
+						<input name="file" type="file" multiple />
+					</div>
+					<div class="form-group" align="center">
+					<input type="submit" name="save" id="save" class="btn btn-info" value="Save" />
+					</div>
+				</form> #}
+				<div class="form-group" id="process" style="display:none;">
+					<div class="progress">
+						<div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuemin="0" aria-valuemax="100" style="">
+						</div>
+					</div>
+				</div>
+			</div>
+		</div><br>
+
 		<div class="row">
 			<div class="col-lg-8" style="padding: 0px 0px;">
 				<div class="container data_upload_panel">
@@ -186,7 +269,7 @@
 									</div>
 								</div>
 								<div class="row data_upload_content" >
-									{{ form_widget(fform.files_to_insert) }}
+									{{ form_widget(fform) }}
 								</div>
 							{{ form_end(fform) }}
 
@@ -262,7 +345,6 @@
 					</div>
 				</div>
 			</div>
-
 		</div>
 		<div class="row" style="margin-top: 15px;">
 			<div class="col-lg-8" style="padding: 0px 0px;">

app/Resources/views/search_result.html.twig

@@ -234,7 +234,20 @@
     					<div id="cy-nav" class="collapse navbar-collapse"
     						style="padding-left: 0px;">
     						<ul id="cy_nav_menu_list" class="nav navbar-nav cy-nav">
-    							<li id="search_dropdown_toggle_li" class="dropdown network_dropdown"><a id="search_dropdown_toggle" href="#">Search <span class="caret"></span></a>
+    							<li id="organism_select_li" class="dropdown network_dropdown"><a id="organism_select_toggle" href="#">Select organism: </a>
+    							</li>
+								<li id="organism_select_form_li" class="dropdown network_dropdown">
+									{{ form_start(organism_form) }}
+										{{ form_widget(organism_form.organism_select) }}
+									{{ form_end(organism_form) }}
+								</li>
+								<li id="organism_info_li">
+									<!-- Button trigger modal -->
+										<button type="button" class="btn btn-primary" data-toggle="modal" data-target="#OrganismInfoModal">
+										Info
+									</button>
+								</li>
+								<li id="search_dropdown_toggle_li" class="dropdown network_dropdown"><a id="search_dropdown_toggle" href="#">Search <span class="caret"></span></a>
     								<ul id="search_tab" class="dropdown-menu">
     									<li style="padding: 20px 0px 10px 0px; min-width: 400px;" class="search_box">
     										<div class="container">
@@ -568,10 +581,31 @@
     						</ul>
     					</div>
     				</div>
+
     			</nav>
     		</div>
-
     </div>
+
+	<!-- Modal -->
+	<div class="modal fade" id="OrganismInfoModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
+	<div class="modal-dialog" role="document">
+		<div class="modal-content">
+		<div class="modal-header">
+			<h3 class="modal-title" id="exampleModalLabel">Organism Info</h3>
+			<button type="button" class="close" data-dismiss="modal" aria-label="Close">
+			<span aria-hidden="true">&times;</span>
+			</button>
+		</div>
+		<div class="modal-body" id="OrganismInfoModalBody">
+			...
+		</div>
+		<div class="modal-footer">
+			<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+		</div>
+		</div>
+	</div>
+	</div>
+
         <div class="row network_row" >
         		<div>
         			<div id='cy'><div id="no_interactions_found" class="hidden" style="text-align: center; z-index:1000;"><img id="huri_img" width=314 height=188 src="{{ url }}assets/images/huri_image2.png" style="display:none;"/></div></div>			

src/AppBundle/Controller/CreateFolderController.php

@@ -68,6 +68,103 @@ public function CreateFolderAction($dir_name, Request $request)
 
 	}
 
+	/**
+	 * about
+	 * @Route("/createOrganism", name="createOrganism")
+	 * @Route("/admin/createOrganism", name="admin_createOrganism")
+	 * @Method({"GET", "POST"})
+	 */
+	public function CreateOrganismAction(Request $request)
+	{	
+
+
+		$organism_name=$request->query->get('organism_name');
+		$organism_taxid=$request->query->get('tax_id');
+		$organism_description=$request->query->get('organism_description');
+		$organism_scientificName=$request->query->get('scientific_name');
+		$organism_class=$request->query->get('organism_class');
+
+
+		$organism_data=array(
+			'organism_name'=>$organism_name,
+			'organism_taxid'=>$organism_taxid,
+			'organism_description'=>$organism_description,
+			'organism_scientificName'=>$organism_scientificName,
+			'organism_class'=>$organism_class,
+		);
+
+		$functions = $this->get('app.functions');		
+		$connection =  $functions->mysql_connect();
+
+		// $interactor_id_string = join(',', $interactor_array);
+		// $interactor_id_string = "'" . str_replace(",", "','", $interactor_id_string) . "'";
+
+		$query='select * from organism where common_name="'.$organism_name.'"';
+
+		$result = $connection->query($query);
+		// mysqli_close($connection);
+		// $organism_arrays = array();
+		if($result){
+			$count =0;
+			while($row = $result->fetch_assoc()) {
+				$count++;
+			}
+			if ($count>0){
+				$this->addFlash(
+					'success',
+					'Organism already present with the name: ' .$organism_name
+				);
+				$url_new= $this->generateUrl('data_manager');
+				$response = new RedirectResponse($url_new);
+				return $response;
+			}
+		}
+
+		$query='insert into organism (common_name,description,scientific_name,class,taxid_id) VALUES ("';
+		$query=$query.$organism_name.'","'.$organism_description.'","'.$organism_scientificName.'","'.$organism_class.'","'.$organism_taxid.'")';
+
+		$result = $connection->query($query);
+		mysqli_close($connection);
+
+		// $organism_array = array();
+		// foreach ($organism_arrays as $organism) {
+
+		// 	$id = $organism['id'];
+		// 	$common_name = $organism['common_name'];
+		// 	$name=$id.". "."$common_name";
+		// 	$organism_array[] = $name;
+		// }
+		// var_dump($organism_data);
+		// die;
+		// if(!empty($fname)){
+		// 	// dump($fname);die;
+
+		// 	$root=$this->getParameter('kernel.root_dir');
+		// 	$path=$root.$sp_char."..".$sp_char."web".$sp_char."uploads".$sp_char.$fname;
+		// 	$filesystem = new Filesystem();
+		// 	$filesystem->mkdir($path, 0777);
+		// 	// $filesystem->remove($path);	
+		// 	$path=null;
+
+		// 	$url_new= $this->generateUrl('file_manager', ['upload_directory' => $fname]);
+		// 	$response = new RedirectResponse($url_new);
+		// 	return $response;
+		// }
+		// die;
+
+
+		$this->addFlash(
+            'success',
+            'Organism '.$organism_name. ' created successfully!  '
+        );
+
+
+		$url_new= $this->generateUrl('data_manager');
+		$response = new RedirectResponse($url_new);
+		return $response;
+
+	}
+
 
 	/**
 	 * about