From 64a4bdfda3dfc3657f7f3dcdb282936795a26d1a Mon Sep 17 00:00:00 2001
From: genstat <cyril.nerin@pasteur.fr>
Date: Fri, 4 Jun 2021 17:46:48 +0200
Subject: [PATCH 01/25]  FIX #80

---
 jass/static/chromo_heatmap_manhattan.html | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/jass/static/chromo_heatmap_manhattan.html b/jass/static/chromo_heatmap_manhattan.html
index a21806c..dbaceaa 100644
--- a/jass/static/chromo_heatmap_manhattan.html
+++ b/jass/static/chromo_heatmap_manhattan.html
@@ -28,12 +28,9 @@
   <!-- Plotly.js -->
 
 
-   <script src="js/plotly-latest.min.js"></script>   <!--https://cdn.plot.ly/plotly-latest.min.js-->
-   <!--<script src="js/jquery.min.js"></script>	http://ajax.googleapis.com/ajax/libs/
-	
-   jquery/1.8.1/jquery.min.js-->
+   <script src="js/plotly-latest.min.js"></script>   
    <script src="https://code.jquery.com/jquery-3.3.1.js"></script>
-   <script src="js/jquery-ui.js"></script>	<!--https://code.jquery.com/ui/1.12.1/jquery-ui.js-->
+   <script src="js/jquery-ui.js"></script>
 
    <script src="js/snap.svg-min.js"></script>
    <script src="js/Chromosome.js"></script>
@@ -49,7 +46,6 @@
 
 	<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js" ></script>
 
-	<!--<script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" ></script>-->
 	<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>
 	<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap.min.js"></script>
 	<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/select/1.3.0/js/dataTables.select.min.js"></script>
@@ -63,10 +59,6 @@
 	<script src="https://cdn.datatables.net/buttons/1.3.1/js/dataTables.buttons.min.js"></script>
 	<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.3.1/css/buttons.dataTables.min.css">
     <script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.flash.min.js"></script>
-	
-	<script src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-MML-AM_CHTML" type="text/javascript"></script>
-	
-	<!--<script defer language="javascript" src="js/create_genome_full_csv.js" type="text/javascript"> </script>-->
 
 
    <style>
-- 
GitLab


From 519ee3f80c3c6f3edf7f1da7d6d1e9db0fc32e28 Mon Sep 17 00:00:00 2001
From: genstat <cyril.nerin@pasteur.fr>
Date: Fri, 4 Jun 2021 17:47:23 +0200
Subject: [PATCH 02/25]  FIX #80 FEAT #55

---
 jass/static/directLink.html | 249 ++++++++++++++++++++++--------------
 1 file changed, 156 insertions(+), 93 deletions(-)

diff --git a/jass/static/directLink.html b/jass/static/directLink.html
index cb71192..bad989d 100644
--- a/jass/static/directLink.html
+++ b/jass/static/directLink.html
@@ -1,93 +1,156 @@
-<html>
-
- <script src="https://code.jquery.com/jquery-3.2.1.min.js"></script>
-<script src="http://malsup.github.io/jquery.blockUI.js"></script>
-<script>
-function directLink()	{
-	//var phe = ["z_DIAGRAM_T2D", "z_GLG_HDL", "z_GLG_LDL", "z_GLG_TC", "z_GLG_TG"];
-
-
-	//http://jass.pasteur.fr/directLink.html?z_DIAGRAM_T2D,%20z_GLG_HDL,%20z_GLG_LDL,%20z_GLG_TC,%20z_GLG_TG
-
- 	var phes = extractUrlParam();	
-	//phes ="z_PGC_BIP,z_GIANT_BMI";
-	//phes ="z_DIAGRAM_T2D,z_GLG_HDL,z_GLG_LDL,z_GLG_TC,z_GLG_TG";
-	
-	//console.log("!!!!!!!"+phes);
-        //console.log(phes[0])
-	var phe = {};
-        phe['phenotypeID'] =phes;
-	//var phes = extractUrlParams();
-	//phes +="";
-	//var phenotypes = phes.split(',');
-	//var phenotypes = ["z_C4D_CHD","z_CARDIOGRAM_CHD","z_ICBP_DBP"];
-	//var monobjet_json = JSON.stringify(phenotypes);	
-	//console.log(monobjet_json);
-	//sessionStorage.setItem("phenotypes",monobjet_json);
-	//location.href = 'http://hub17.hosting.pasteur.fr/getVar.html';
-	
- 	//var test =extractUrlParams();	
-	//console.log(test);
-	
-	//console.log(extractUrlParams());
-	//location.href = 'chromo_heatmap_manhattan.html';
-                                        $.blockUI({ css: {
-                                            border: 'none',
-                                            padding: '15px',
-                                            backgroundColor: '#000',
-                                            '-webkit-border-radius': '10px',
-                                            '-moz-border-radius': '10px',
-                                            opacity: .5,
-                                            color: '#fff'} });
-
-                                        var status="-1";
-                                        var getProjectStatus = function(){
-						//$.post( "/api/projects",{'phenotypeID':"z_DIAGRAM_T2D,z_GLG_HDL,z_GLG_LDL,z_GLG_TC,z_GLG_TG"}).done(function( data ) {
-                                                $.post( "/api/projects",phe).done(function( data ) {
-                                                        status = data.status.worktable;
-                                                        console.log("!! status "+status);
-                                                        if(status =="READY"){
-                                                                $.unblockUI();
-                                                                console.log( data );
-                                                                sessionStorage.setItem("id",data.id);
-                                                                console.log(data.phenotypes);
-                                                                //var monobjet_json = JSON.stringify(data.phenotypes[0]);
-                                                                var monobjet_json = JSON.stringify(data.phenotypes);
-                                                                sessionStorage.setItem("phenotypes",monobjet_json);
-                                                                console.log(data.phenotypes[0]["cohort"]);
-                                                                //location.href = 'http://hub17.hosting.pasteur.fr/getVar.html';
-                                                                location.href = 'chromo_heatmap_manhattan.html';
-                                                        }
-                                                        else if(status =="CREATING"){
-                                                                console.log("CREATING");
-                                                                setTimeout(getProjectStatus, 10000);
-                                                        }
-                                                });
-
-                                        };
-                                        getProjectStatus();
-	
-}
-
-function extractUrlParam(){   
-	var t = location.search.substring(1).split('=');
-	return t[1];
-}
-function extractUrlParams(){   
-    console.log(location.search);
-    var t = location.search.substring(1).split('&');
-    var f = [];
-    for (var i=0; i<t.length; i++){
-        var x = t[ i ].split('=');
-        f[x[0]]=x[1];
-    }
-    return f;
-}
-	
-</script>
-
-<body onload="directLink()">
-
-</body>
-
-</html>
+<html>
+
+<style>	
+	div.blockMe { padding: 30px; margin: 30px; border: 10px solid #ccc; background-color: #ffd }
+	#question { background-color: #ffc; padding: 10px; }
+	#question input { width: 4em ; }
+</style>
+
+<script src="https://code.jquery.com/jquery-3.2.1.min.js"></script>
+<script src="https://malsup.github.io/jquery.blockUI.js"></script>
+
+<script>
+	function avancement() {
+		var ava = document.getElementById("avancement");
+		var prc = document.getElementById("pourcentage");
+		prc.innerHTML = ava.value + "%";
+	}
+	
+	function modif(val) {
+		var ava = document.getElementById("avancement");
+		if((ava.value+val)<=ava.max && (ava.value+val)>0) {
+			ava.value += val;
+		}
+		avancement();
+	}
+	
+	function directLink() {
+		var toApply = 1;
+		var phe = {};
+		var url = new URL(window.location.toString());
+		var search_params = new URLSearchParams(url.search);
+		
+		if (search_params.has("phenotypes")) {
+			var phes = search_params.get("phenotypes");
+			phe['phenotypeID'] = phes;
+			if (phes == '') {
+				selectedNumber = 0;
+			}
+			else {			
+				selectedNumber = (phes.split(",")).length;
+			}
+			console.log("phes='"+phes+"'");
+			console.log("selectedNumber="+selectedNumber);
+			if (selectedNumber == 0){
+				// WARNING: No phenotype is selected !
+				var User_Message = "𝐖𝐀𝐑𝐍𝐈𝐍𝐆: 𝐏𝐥𝐞𝐚𝐬𝐞 𝐜𝐡𝐨𝐨𝐬𝐞 𝐚𝐧 𝐚𝐫𝐫𝐚𝐲 𝐨𝐟 𝐏𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞𝐬..."
+				alert(User_Message);
+				toApply = 0;
+			}
+			else if (selectedNumber == 1){
+				//  A confirmation window is displayed
+				var User_Message = "𝐖𝐀𝐑𝐍𝐈𝐍𝐆: 𝐲𝐨𝐮 𝐡𝐚𝐯𝐞 𝐬𝐞𝐥𝐞𝐜𝐭𝐞𝐝 𝐨𝐧𝐥𝐲 𝐨𝐧𝐞 𝐩𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞!" +
+				"\nIt isn't the way JASS normally works.\nDo you want to continue?";
+				var r = confirm(User_Message);					
+				if (r == true) { // Button OK is selected
+					toApply = 1;
+				} else { // Button CANCEL is selected
+					toApply = 0;
+				}
+			}
+			else if ((selectedNumber > 20) && (selectedNumber <= 64)){
+				//  A confirmation window is displayed
+				var User_Message = "𝐖𝐀𝐑𝐍𝐈𝐍𝐆: 𝐲𝐨𝐮 𝐡𝐚𝐯𝐞 𝐬𝐞𝐥𝐞𝐜𝐭𝐞𝐝 " + 
+				selectedNumber + 
+				" 𝐩𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞𝐬!\nThe computation will be very long. \nDo you want to continue?";
+				var g = confirm(User_Message);
+				if (g == true) { // Button OK is selected
+					toApply = 1;
+				} else { // Button CANCEL is selected
+					toApply = 0;
+				}
+			}
+			else if (selectedNumber > 64) {
+				// ERROR: More than 64 Phenotypes have been selected !
+				var User_Message = "𝐄𝐑𝐑𝐎𝐑: 𝐲𝐨𝐮 𝐡𝐚𝐯𝐞 𝐬𝐞𝐥𝐞𝐜𝐭𝐞𝐝 " +
+				selectedNumber + 
+				" 𝐩𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞𝐬!\nThe current implementation of JASS cannot analyze more than 64 phenotypes.";
+				alert(User_Message);
+				toApply = 0;
+			}
+		}
+		else {
+			// WARNING: No phenotype is selected !
+			var User_Message = "𝐖𝐀𝐑𝐍𝐈𝐍𝐆: 𝐏𝐥𝐞𝐚𝐬𝐞 𝐜𝐡𝐨𝐨𝐬𝐞 𝐚𝐧 𝐚𝐫𝐫𝐚𝐲 𝐨𝐟 𝐏𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞𝐬..."
+			alert(User_Message);
+			toApply = 0;
+		}
+		
+		if (toApply == 1){
+			if (search_params.has("chromosome")) {
+				var chromosome = search_params.get("chromosome");
+				// Local analysis
+				var User_Message = 
+				"Local analysis is not yet implemented in this version of JASS." +
+				"\nDo not specify a chromosome number and start and end positions";
+				alert(User_Message);
+				toApply = 0;			
+				// var Page_to_display = "chromo_heatmap_manhattan_by_region.html"			
+			}
+			else {
+				// Whole genome analysis
+				var Page_to_display = "chromo_heatmap_manhattan.html"
+			}
+		
+			if(search_params.has("start")) {
+				var start = search_params.get("start");
+			}
+		
+			if(search_params.has("end")) {
+				var end = search_params.get("end");
+			}
+		}
+		
+		if (toApply == 1){
+			$.blockUI({ message: $('#question'), css: { width: '275px' }});
+			avancement(); //Initialisation
+					
+			var status = "-1";
+			var JASS_progress = 0;
+			var Old_progress = 0;
+			var getProjectStatus = function(){
+				$.post( "/api/projects",phe).done(function( data ) {
+					status = data.status.worktable;
+					JASS_progress = data.progress;
+					var deltaProgress = JASS_progress - Old_progress;
+					Old_progress = JASS_progress;
+					modif(deltaProgress);
+					
+					if(status == "READY"){
+						$.unblockUI();	
+						sessionStorage.setItem("id",data.id);
+						var monobjet_json = JSON.stringify(data.phenotypes);	
+						sessionStorage.setItem("phenotypes",monobjet_json);
+						location.href = Page_to_display;
+					}
+					else if(status == "CREATING"){																		
+						setTimeout(getProjectStatus, 10000);	
+					}
+				});			
+			};
+			getProjectStatus();	
+		}
+	}
+	
+</script>
+
+<body onload="directLink()">
+	<div id="question" style="display:none; cursor: default">
+    <H3>Analysis in progress ...</H3>
+	<progress id="avancement" value="0" max="100"></progress>
+	<span id="pourcentage"></span>
+</div>
+
+</body>
+
+</html>
-- 
GitLab


From e95c93374c1a337c63a6caa9dccc1d11eb5f90a6 Mon Sep 17 00:00:00 2001
From: genstat <cyril.nerin@pasteur.fr>
Date: Fri, 4 Jun 2021 17:47:51 +0200
Subject: [PATCH 03/25] FIX #80

---
 jass/static/export.html | 372 ++++++++++++++++++----------------------
 1 file changed, 171 insertions(+), 201 deletions(-)

diff --git a/jass/static/export.html b/jass/static/export.html
index 23f4666..969381c 100644
--- a/jass/static/export.html
+++ b/jass/static/export.html
@@ -1,201 +1,171 @@
-<html>
-
-<head>
-    <script src="js/jquery.min.js"></script>   <!--https://cdn.plot.ly/plotly-latest.min.js-->
-    <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>   <!--https://cdn.plot.ly/plotly-latest.min.js-->
-    <!--<script src="http://tablesorter.com/addons/pager/jquery.tablesorter.pager.js"></script>-->
-    <!-- <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/1.10.15/css/jquery.dataTables.css"> -->
-
-
-    <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.15/css/jquery.dataTables.min.css">
-    <script type="text/javascript" charset="utf8" src="//cdn.datatables.net/1.10.15/js/jquery.dataTables.js"></script>
-
-    
-
-    	<!-- datatables buttons pdf csv copy -->
-	<script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script>
-	<script src="js/pdfmake.min.js"></script>
-	<script src="js/vfs_fonts.js"></script>
-	<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.html5.min.js"></script>
-	<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.print.min.js"></script>
-	<script src="https://cdn.datatables.net/buttons/1.3.1/js/dataTables.buttons.min.js"></script>
-	<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.3.1/css/buttons.dataTables.min.css">
-        <script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.flash.min.js"></script>
-
-    <script src="http://malsup.github.io/jquery.blockUI.js"></script>
-    <link rel="stylesheet" href="http://ajax.googleapis.com/ajax/libs/jqueryui/1/themes/smoothness/jquery-ui.css">
-    <link rel="stylesheet" href="https://research.pasteur.fr/wp-content/themes/biologyx2/style.css" type="text/css" >
-    <style>
-	.header {
-    		margin:0 0 30px 0;
-    		padding: 5px 0 0 0 ;
-			height:50;
-			background-image: url('/static/img/bkg_part2_wthLabel.jpg');
-			background-color: transparent;
-			background-size:contain;
-			object-fit: contain;
-			background-repeat:no-repeat;
-	}	
-	#image-top {height:80!important}
-	</style>
-
-    <script>
-
-
-        var selected = [];
-
-        //goToURL();
-    	var typeExport = sessionStorage.getItem("typeExport");
-
-    	var idProject = sessionStorage.getItem("id");
-		console.log(idProject);
-		var selectedRegion = sessionStorage.getItem("selectedRegion");
-		var selectedChr = sessionStorage.getItem("selectedChr");
-
-		console.log(selectedRegion);
-		console.log(selectedChr);
-    	if(typeExport =="localStat"){
-    		
-			Plotly.d3.csv("/api/projects/"+idProject+"/manhattan/"+selectedChr+"/"+selectedRegion, function(data){ processExportJASSPVAL(data) } );
-	    	}
-    	else if (typeExport =="globalStat"){
-    		Plotly.d3.csv("/api/projects/"+idProject+"/genome", 
-    			function(data){ processExportGJASSPVAL(data)});
-		}
-    	
-    	else if(typeExport =="heatmap"){
-    		Plotly.d3.csv("/api/projects/"+idProject+"/heatmap/"+selectedChr+"/"+selectedRegion, 
-    			 function(data){ processExportHeatmap(data) } ); 	
-    	}
-
-    	function processExportGJASSPVAL(rows) {
-			console.log("processExportGJASSPVAL rows.length "+rows.length);
-			console.log(rows[0]);
-			var columns =["CHR","JOSTmin","MiddlePosition","PVALmin","Region","snp_ids"]
-
-			tabulate(rows,columns);
-		}
-
-    	function processExportHeatmap(rows) {
-			console.log("processExportHeatmap rows.length "+rows.length);
-
-			var columns =["Region","CHR","position","snp_ids","JASS_PVAL"];
-			tabulate(rows,columns);
-		}
-
-	function processExportJASSPVAL(rows) {
-		console.log("processExportJASSPVAL rows.length "+rows.length);
-
-		var columns =["Region","CHR","position","snp_ids","JASS_PVAL"];
-			tabulate(rows,columns);
-	}
-		
-   		
-
-   	function tabulate(data, columns) {
-                  console.log(data);
-
-                   //var table = document.createElement("table");
-                  var table = $('#pheTable');
-                   //table.id="pheTable";  
-                  var thead = document.createElement("thead");
-                  var tr = document.createElement("tr");
-                  for (var i=0; i<columns.length; i++) {
-                    	if ((columns[i] != "ID")&&(columns[i] != "linkRef")){
-	                        var th = document.createElement("th");
-	                        th.innerHTML =columns[i];
-	                        tr.appendChild(th);
-	                    }
-                  }
-                    //var th = document.createElement("th");
-                    //th.innerHTML ="Select";
-                    //thead.appendChild(th);
-                    thead.appendChild(tr);
-                    table.append(thead);
-
-                    //console.log(table);
-                    //var idCounter=1;
-                    var tbody = document.createElement("tbody");
-                    for (var i=0; i<data.length; i++) {
-                        //for (var j=0; j<columns.length; j++) {
-                            //console.log(data[i]);
-                        //console.log("id "+data[i]['ID']);
-                        //}
-                        var tr = document.createElement("tr");
-                        //var val = data[i]['ID'];
-                        //var linkRef =  data[i]['linkRef'];
-						
-                        for (var j=0; j<columns.length; j++) {
-                            var td  = document.createElement("td");
-                            td.innerHTML=data[i][columns[j]];
-							tr.append(td);
-			            }
-                        //var td  = document.createElement("td");
-                        //td.innerHTML='-';
-                        //var val = data[i]['ID'];
-                	//	td.innerHTML= "<input id='chk_" + idCounter + "' name ='type' type='checkbox' value='" + val + "' />";
-                	//	idCounter ++;
-                        //tr.append(td);
-                        tbody.appendChild(tr);
-                    }
-
-                    table.append(tbody);
-
-                //header1.setAttribute("class", "header1" );
-                //return table;
-
-                var tmpArray =new Array();
-                for (var j=0; j<columns.length; j++) {
-                    tmpArray.push({});
-                }
-		
-                var table = $('#pheTable').dataTable( {
-            
-                	aoColumns: tmpArray,
-                	dom: 'Bfrtip',
-        			buttons: [
-            			'copy', 'csv', 'pdf'
-       				]
-
-            
-            	} );
-
-            	//'copy', 'csv', 'excel', 'pdf'
-            	/*new $.fn.dataTable.Buttons( table, {
-       				 buttons: [
-          			  {
-			                text: 'Button 2',
-			                action: function ( e, dt, node, conf ) {
-			                    alert( 'Button 2 clicked on' );
-			                }
-			            },
-			            {
-			                text: 'Button 3',
-			                action: function ( e, dt, node, conf ) {
-			                    alert( 'Button 3 clicked on' );
-			                }
-			            }
-        			]
-
-    			} );*/
-    			
-    } 
-
-        
-
-    </script>
-</head>
-
-<body>
-
-<div class="header" > </div>
-
-<h2>Data Table Export</h2>
-
-<div id='divContainer' width ="400px">
-	<table id ="pheTable" style="width :500px" class="display dataTable"></table>
-</div>
-<!-- <button id="btn1">Export</button> -->
-</body>
-
-</html>
+<html>
+
+<head>
+    <script src="js/jquery.min.js"></script>
+    <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>   
+
+    <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.15/css/jquery.dataTables.min.css">
+    <script type="text/javascript" charset="utf8" src="//cdn.datatables.net/1.10.15/js/jquery.dataTables.js"></script>
+
+    
+
+    	<!-- datatables buttons pdf csv copy -->
+	<script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script>
+	<script src="js/pdfmake.min.js"></script>
+	<script src="js/vfs_fonts.js"></script>
+	<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.html5.min.js"></script>
+	<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.print.min.js"></script>
+	<script src="https://cdn.datatables.net/buttons/1.3.1/js/dataTables.buttons.min.js"></script>
+	<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.3.1/css/buttons.dataTables.min.css">
+        <script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.flash.min.js"></script>
+
+    <script src="https://malsup.github.io/jquery.blockUI.js"></script>
+    <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1/themes/smoothness/jquery-ui.css">
+    <link rel="stylesheet" href="https://research.pasteur.fr/wp-content/themes/biologyx2/style.css" type="text/css" >
+    <style>
+	.header {
+    		margin:0 0 30px 0;
+    		padding: 5px 0 0 0 ;
+			height:50;
+			background-image: url('/static/img/bkg_part2_wthLabel.jpg');
+			background-color: transparent;
+			background-size:contain;
+			object-fit: contain;
+			background-repeat:no-repeat;
+	}	
+	#image-top {height:80!important}
+	</style>
+
+    <script>
+
+
+        var selected = [];
+
+    	var typeExport = sessionStorage.getItem("typeExport");
+
+    	var idProject = sessionStorage.getItem("id");
+		console.log(idProject);
+		var selectedRegion = sessionStorage.getItem("selectedRegion");
+		var selectedChr = sessionStorage.getItem("selectedChr");
+
+		console.log(selectedRegion);
+		console.log(selectedChr);
+    	if(typeExport =="localStat"){
+    		
+			Plotly.d3.csv("/api/projects/"+idProject+"/manhattan/"+selectedChr+"/"+selectedRegion, function(data){ processExportJASSPVAL(data) } );
+	    	}
+    	else if (typeExport =="globalStat"){
+    		Plotly.d3.csv("/api/projects/"+idProject+"/genome", 
+    			function(data){ processExportGJASSPVAL(data)});
+		}
+    	
+    	else if(typeExport =="heatmap"){
+    		Plotly.d3.csv("/api/projects/"+idProject+"/heatmap/"+selectedChr+"/"+selectedRegion, 
+    			 function(data){ processExportHeatmap(data) } ); 	
+    	}
+
+    	function processExportGJASSPVAL(rows) {
+			console.log("processExportGJASSPVAL rows.length "+rows.length);
+			console.log(rows[0]);
+			var columns =["CHR","JOSTmin","MiddlePosition","PVALmin","Region","snp_ids"]
+
+			tabulate(rows,columns);
+		}
+
+    	function processExportHeatmap(rows) {
+			console.log("processExportHeatmap rows.length "+rows.length);
+
+			var columns =["Region","CHR","position","snp_ids","JASS_PVAL"];
+			tabulate(rows,columns);
+		}
+
+	function processExportJASSPVAL(rows) {
+		console.log("processExportJASSPVAL rows.length "+rows.length);
+
+		var columns =["Region","CHR","position","snp_ids","JASS_PVAL"];
+			tabulate(rows,columns);
+	}
+		
+   		
+
+   	function tabulate(data, columns) {
+                  console.log(data);
+
+                  var table = $('#pheTable');  
+                  var thead = document.createElement("thead");
+                  var tr = document.createElement("tr");
+                  for (var i=0; i<columns.length; i++) {
+                    	if ((columns[i] != "ID")&&(columns[i] != "linkRef")){
+	                        var th = document.createElement("th");
+	                        th.innerHTML =columns[i];
+	                        tr.appendChild(th);
+	                    }
+                  }
+
+                    thead.appendChild(tr);
+                    table.append(thead);
+
+                    var tbody = document.createElement("tbody");
+                    for (var i=0; i<data.length; i++) {
+
+                        var tr = document.createElement("tr");
+						
+                        for (var j=0; j<columns.length; j++) {
+                            var td  = document.createElement("td");
+                            td.innerHTML=data[i][columns[j]];
+							tr.append(td);
+			            }
+
+                        tbody.appendChild(tr);
+                    }
+
+                    table.append(tbody);
+
+
+                var tmpArray =new Array();
+                for (var j=0; j<columns.length; j++) {
+                    tmpArray.push({});
+                }
+		
+                var table = $('#pheTable').dataTable( {
+            
+                	aoColumns: tmpArray,
+                	dom: 'Bfrtip',
+        			buttons: [ {
+            			 extend: 'csv',
+
+						text : 'Export to CSV',
+
+						filename: function(){
+
+							var d = new Date();
+
+							var n = d.getTime();
+
+							return 'Data_Table';
+
+						},
+       				}]
+					            
+            	} );
+    			
+    } 
+
+        
+
+    </script>
+</head>
+
+<body>
+
+<div class="header" > </div>
+
+<h2>Data Table Export</h2>
+
+<div id='divContainer' width ="400px">
+	<table id ="pheTable" style="width :500px" class="display dataTable"></table>
+</div>
+
+</body>
+
+</html>
-- 
GitLab


From 053ef2798dcc0b8f90a44b197ded950bbe01f6e7 Mon Sep 17 00:00:00 2001
From: genstat <cyril.nerin@pasteur.fr>
Date: Fri, 4 Jun 2021 17:48:15 +0200
Subject: [PATCH 04/25] FIX #80

---
 jass/static/selectPhenotypes.html | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/jass/static/selectPhenotypes.html b/jass/static/selectPhenotypes.html
index a49e381..3971722 100644
--- a/jass/static/selectPhenotypes.html
+++ b/jass/static/selectPhenotypes.html
@@ -7,7 +7,7 @@
     <link rel="stylesheet" type="text/css" href="/css/jquery.dataTables.min.css">
     <script type="text/javascript" charset="utf8" src="/js/jquery.dataTables.js"></script>
     <script src="/js/jquery.blockUI.js"></script>
-    <link rel="stylesheet" href="http://ajax.googleapis.com/ajax/libs/jqueryui/1/themes/smoothness/jquery-ui.css">
+    <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1/themes/smoothness/jquery-ui.css">
     <link rel="stylesheet" href="https://research.pasteur.fr/wp-content/themes/biologyx2/style.css" type="text/css" >
     <style>
 	.header {
@@ -180,11 +180,9 @@
 			   					    console.log( data );
 									sessionStorage.setItem("id",data.id);
 									console.log(data.phenotypes);
-									//var monobjet_json = JSON.stringify(data.phenotypes[0]);
-										var monobjet_json = JSON.stringify(data.phenotypes);	
+									var monobjet_json = JSON.stringify(data.phenotypes);	
 									sessionStorage.setItem("phenotypes",monobjet_json);
 									console.log(data.phenotypes[0]["cohort"]);
-									//location.href = 'http://hub17.hosting.pasteur.fr/getVar.html';
 									location.href = 'chromo_heatmap_manhattan.html';
 								}
 								else if(status =="CREATING"){
-- 
GitLab


From ac747ef62f86ec136fe851abcf3333b785524b19 Mon Sep 17 00:00:00 2001
From: genstat <cyril.nerin@pasteur.fr>
Date: Fri, 4 Jun 2021 17:53:15 +0200
Subject: [PATCH 05/25]  FIX #80

---
 jass/static/index.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/jass/static/index.html b/jass/static/index.html
index 9f514a8..07cbf37 100644
--- a/jass/static/index.html
+++ b/jass/static/index.html
@@ -55,15 +55,15 @@
   <div id="tabs-3">
 	<p><b>JASS: command line and web interface for the joint analysis of GWAS results</b><br />
 	Hanna Julienne, Pierre Lechat, Vincent Guillemot, Carla Lasry, Chunzi Yao, Robinson Araud, Vincent Laville, Bjarni Vilhjalmsson, Hervé Ménager, Hugues Aschard<br />
-	in: NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa003, <a href="https://doi.org/10.1093/nargab/lqaa003"> <FONT color=#0000FF>https://doi.org/10.1093/nargab/lqaa003</FONT></a></p>
+	in: NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa003, <a href="https://urldefense.com/v3/__https://doi.org/10.1093/nargab/lqaa003__;!!JFdNOqOXpB6UZW0!75infPACk5lQWcBTD-rE5FQb6Yk4WckKROxH7a5qa4ERTDyiliWfWLGe8-HIgjvh3Gk$"> <FONT color=#0000FF>https://doi.org/10.1093/nargab/lqaa003</FONT></a></p>
 	<p><b>Multitrait genetic-phenotype associations to connect disease variants and biological mechanisms</b><br />
 	Hanna Julienne, Vincent Laville, Zachary R. McCaw, Zihuai He, Vincent Guillemot, Carla Lasry, Andrey Ziyatdinov, Amaury Vaysse, Pierre Lechat, Hervé Ménager, Wilfried Le Goff, Marie-Pierre Dube, Peter Kraft, Iuliana Ionita-Laza, Bjarni J. Vilhjálmsson, Hugues Aschard<br />
-	preprint in: biorxiv, <a href=https://www.biorxiv.org/content/10.1101/2020.06.26.172999v1.full> <FONT color=#0000FF>https://www.biorxiv.org/content/10.1101/2020.06.26.172999v1.full</FONT></a></p>
+	preprint in: biorxiv, <a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.06.26.172999v1.full__;!!JFdNOqOXpB6UZW0!75infPACk5lQWcBTD-rE5FQb6Yk4WckKROxH7a5qa4ERTDyiliWfWLGe8-HIV8Z7Cco$"> <FONT color=#0000FF>https://www.biorxiv.org/content/10.1101/2020.06.26.172999v1.full</FONT></a></p>
   </div>
 </div>
 </body>
 
 <footer id="colophon" class="site-footer" role="contentinfo">
-<a href="http://www.pasteur.fr/en" target="_blank"><div id="footlogo"></div></a>
+<a href="https://www.pasteur.fr/en" target="_blank"><div id="footlogo"></div></a>
 </footer>
 </html>
-- 
GitLab


From 2436f00310d6ce0e240a7323b57f2cf960cb7e88 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Wed, 9 Jun 2021 16:50:01 +0200
Subject: [PATCH 06/25] apply changes in deps management from dev branch.

---
 requirements.txt |  2 +-
 setup.py         | 13 ++++++++++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 4d1144b..25400d9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-git+https://github.com/hmenager/connexion.git#egg=connexion[swagger-ui]
+git+https://github.com/hmenager/connexion.git@master#egg=connexion[swagger-ui]
 aiohttp
 python_dateutil
 setuptools
diff --git a/setup.py b/setup.py
index 42e05c5..19675e5 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,18 @@ SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, 'README.md')
 readme = open(README).read()
 
-REQUIRES = ["connexion", "python_dateutil", "setuptools", "pandas", "tables", "scipy", "matplotlib", "celery", "h5py", "aiohttp", "numpy"]
+REQUIRES = [
+    "connexion[swagger-ui] @ git+https://github.com/hmenager/connexion.git@master#egg=connexion[swagger-ui]",
+    "aiohttp",
+    "python_dateutil",
+    "setuptools",
+    "numpy",
+    "pandas",
+    "tables",
+    "scipy",
+    "matplotlib",
+    "celery",
+]
 
 setup(
     name=NAME,
-- 
GitLab


From f67a0800202f0682c608ea5c6bd7bc4eaa99b41d Mon Sep 17 00:00:00 2001
From: Hanna  JULIENNE <hanna.julienne@pasteur.fr>
Date: Wed, 9 Jun 2021 17:39:22 +0200
Subject: [PATCH 07/25] change default handling of missing value : the server
 and the command line will keep SNPs with missing phenotypes

---
 jass/__main__.py | 60 ++++++++++++++++++++++++------------------------
 1 file changed, 30 insertions(+), 30 deletions(-)

diff --git a/jass/__main__.py b/jass/__main__.py
index 78f4010..27b0e25 100644
--- a/jass/__main__.py
+++ b/jass/__main__.py
@@ -32,32 +32,32 @@ def absolute_path_of_the_file(fileName, output_file = False):
         if (Directory_path_exist == False):
             # Test the path using the Jass data directory
             absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName))
-            
+
             Directory_path_exist = os.path.exists(os.path.dirname(absoluteFilePath))
-        
+
         if (Directory_path_exist == False):
             Message = "The directory of the file {} does not exist".format(fileName)
             raise NameError(Message)
     else:
         # Test if the file path exist
         File_path_exist = os.path.exists(absoluteFilePath)
-    
+
         if (File_path_exist == False):
             # Test the path using the Jass data directory
             absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName))
             File_path_exist = os.path.exists(absoluteFilePath)
-        
+
         if (File_path_exist == False):
             Message = "The file {} does not exist".format(fileName)
             raise NameError(Message)
-        
+
         # Test if it is realy a file
         Is_a_file = os.path.isfile(absoluteFilePath)
-        
+
         if (not Is_a_file) :
             Message = "{} is not a file".format(fileName)
             raise NameError(Message)
-            
+
     return absoluteFilePath
 
 
@@ -72,7 +72,7 @@ def w_list_phenotypes(args):
 
 
 def compute_worktable(args):
-    
+
     csv_file_path = args.csv_file_path
     if (csv_file_path is not None):
         csv_file_path = absolute_path_of_the_file(csv_file_path, True)
@@ -82,7 +82,7 @@ def compute_worktable(args):
     remove_nan = not (args.keep_nans)
     significance_treshold = float(args.significance_treshold)
     post_filtering = bool(args.post_filtering)
-    custom_loadings = args.custom_loadings    
+    custom_loadings = args.custom_loadings
     chromosome = args.chromosome_number
     pos_Start = args.start_position
     pos_End = args.end_position
@@ -99,10 +99,10 @@ def compute_worktable(args):
         strategy = args.strategy
 
     create_worktable_file(
-        phenotype_ids = selected_phenotypes, 
-        init_file_path = init_table_path, 
+        phenotype_ids = selected_phenotypes,
+        init_file_path = init_table_path,
         project_hdf_path = worktable_path,
-        remove_nan = remove_nan, 
+        remove_nan = remove_nan,
         stat = strategy,
         optim_na = True,
         csv_file = csv_file_path,
@@ -125,8 +125,8 @@ def w_create_project_data(args):
     manhattan_plot_path = absolute_path_of_the_file(args.manhattan_plot_path, True)
     quadrant_plot_path = absolute_path_of_the_file(args.quadrant_plot_path, True)
     create_global_plot(worktable_path, manhattan_plot_path)
-    create_quadrant_plot(worktable_path, 
-                         quadrant_plot_path, 
+    create_quadrant_plot(worktable_path,
+                         quadrant_plot_path,
                          significance_treshold = float(args.significance_treshold))
 
 
@@ -136,7 +136,7 @@ def w_create_inittable(args):
     regions_map_path = absolute_path_of_the_file(args.regions_map_path)
     description_file_path = absolute_path_of_the_file(args.description_file_path)
     init_table_path = absolute_path_of_the_file(args.init_table_path, True)
-    
+
     create_inittable_file(
         input_data_path,
         regions_map_path,
@@ -155,8 +155,8 @@ def w_plot_quadrant(args):
     worktable_path = absolute_path_of_the_file(args.worktable_path)
     plot_path = absolute_path_of_the_file(args.plot_path)
     significance_treshold = float(args.significance_treshold)
-    create_quadrant_plot(worktable_path, 
-                         plot_path, 
+    create_quadrant_plot(worktable_path,
+                         plot_path,
                          significance_treshold=significance_treshold)
 
 
@@ -197,7 +197,7 @@ def get_parser():
     parser_create_pd.add_argument(
         "--worktable-path", required=True, help="path to the worktable file to generate"
     )
-    parser_create_pd.add_argument("--keep-nans", action="store_true", default=False)
+    parser_create_pd.add_argument("--keep-nans", action="store_true", default=True)
     parser_create_pd.add_argument(
         "--manhattan-plot-path",
         required=True,
@@ -237,7 +237,7 @@ def get_parser():
         required=False,
         help="path to the results file in csv format"
     )
-    
+
     parser_create_pd.add_argument(
         "--chromosome-number",
         required=False,
@@ -255,7 +255,7 @@ def get_parser():
         required=False,
         help="option used only for local analysis: end position of the region studied"
     )
-  
+
     strategies = parser_create_pd.add_mutually_exclusive_group()
     strategies.add_argument("--omnibus", action="store_true", default=True)
     strategies.add_argument("--sumz", action="store_true", default=False)
@@ -336,15 +336,15 @@ def get_parser():
         required=False,
         help="path to the results file in csv format"
     )
-    
+
     parser_create_wt.add_argument(
         "--chunk-size",
         required=False,
         default=50,
         help="Number of region to load in memory at once",
     )
-    
-    parser_create_wt.add_argument("--keep-nans", action="store_true", default=False)
+
+    parser_create_wt.add_argument("--keep-nans", action="store_true", default=True)
 
     parser_create_wt.add_argument(
         "--chromosome-number",
@@ -363,14 +363,14 @@ def get_parser():
         required=False,
         help="option used only for local analysis: end position of the region studied"
     )
-        
+
     strategies = parser_create_wt.add_mutually_exclusive_group()
     strategies.add_argument("--omnibus", action="store_true", default=True)
     strategies.add_argument("--sumz", action="store_true", default=False)
     strategies.add_argument("--fisher_test", action="store_true", default=False)
     strategies.add_argument("--meta_analysis", action="store_true", default=False)
     strategies.add_argument("--strategy")
-    
+
     parser_create_wt.set_defaults(func=w_create_worktable)
 
     # ------- plot-manhattan -------
@@ -385,8 +385,8 @@ def get_parser():
         help="path to the worktable file containing the data",
     )
     parser_create_mp.add_argument(
-        "--plot-path", 
-        required=True, 
+        "--plot-path",
+        required=True,
         help="path to the manhattan plot file to generate"
     )
     parser_create_mp.set_defaults(func=w_plot_manhattan)
@@ -402,8 +402,8 @@ def get_parser():
         help="path to the worktable file containing the data",
     )
     parser_create_mp.add_argument(
-        "--plot-path", 
-        required=True, 
+        "--plot-path",
+        required=True,
         help="path to the quadrant plot file to generate"
     )
     parser_create_mp.add_argument(
@@ -412,7 +412,7 @@ def get_parser():
         help="threshold at which a p-value is considered significant"
     )
     parser_create_mp.set_defaults(func=w_plot_quadrant)
-    
+
     return parser
 
 
-- 
GitLab


From 9dc76727b6c69b7bec39a07af84f0e7def0374e4 Mon Sep 17 00:00:00 2001
From: Hanna  JULIENNE <hanna.julienne@pasteur.fr>
Date: Wed, 9 Jun 2021 19:05:47 +0200
Subject: [PATCH 08/25] change the --keep-nans argument to --remove-nans to
 change defaults behaviour

---
 jass/__main__.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/jass/__main__.py b/jass/__main__.py
index 27b0e25..743b290 100644
--- a/jass/__main__.py
+++ b/jass/__main__.py
@@ -79,7 +79,7 @@ def compute_worktable(args):
     init_table_path = absolute_path_of_the_file(args.init_table_path)
     worktable_path = absolute_path_of_the_file(args.worktable_path, True)
     selected_phenotypes = args.phenotypes
-    remove_nan = not (args.keep_nans)
+    remove_nan = (args.remove_nans)
     significance_treshold = float(args.significance_treshold)
     post_filtering = bool(args.post_filtering)
     custom_loadings = args.custom_loadings
@@ -197,7 +197,7 @@ def get_parser():
     parser_create_pd.add_argument(
         "--worktable-path", required=True, help="path to the worktable file to generate"
     )
-    parser_create_pd.add_argument("--keep-nans", action="store_true", default=True)
+    parser_create_pd.add_argument("--remove-nans", action="store_true", default=False)
     parser_create_pd.add_argument(
         "--manhattan-plot-path",
         required=True,
@@ -344,7 +344,7 @@ def get_parser():
         help="Number of region to load in memory at once",
     )
 
-    parser_create_wt.add_argument("--keep-nans", action="store_true", default=True)
+    parser_create_wt.add_argument("--remove-nans", action="store_true", default=False)
 
     parser_create_wt.add_argument(
         "--chromosome-number",
-- 
GitLab


From fa9c31e3a3c9086c3b8189f270ddb81a0ba4fd6c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Sat, 19 Jun 2021 21:33:51 +0200
Subject: [PATCH 09/25] replace connexion library with flask-smorest

---
 jass/__main__.py                              |   6 +-
 jass/controllers/__init__.py                  |   1 -
 jass/encoder.py                               |  25 --
 jass/models/project.py                        |   3 +-
 jass/models/worktable.py                      |   2 +
 jass/server.py                                | 312 +++++++++++++++++-
 jass/swagger/swagger.yaml                     |  14 -
 jass/test/__init__.py                         |  22 +-
 ...t_default_controller.py => test_server.py} |  13 +-
 requirements.txt                              |   2 +-
 setup.py                                      |   2 +-
 11 files changed, 327 insertions(+), 75 deletions(-)
 delete mode 100644 jass/encoder.py
 rename jass/test/{test_default_controller.py => test_server.py} (52%)

diff --git a/jass/__main__.py b/jass/__main__.py
index 78f4010..bba3a99 100644
--- a/jass/__main__.py
+++ b/jass/__main__.py
@@ -4,7 +4,7 @@
 import os
 import argparse
 
-from jass.server import get_jass_app
+from jass.server import jass_app
 from jass.config import config
 
 from jass.models.phenotype import get_available_phenotypes
@@ -62,8 +62,8 @@ def absolute_path_of_the_file(fileName, output_file = False):
 
 
 def serve(args):
-    app = get_jass_app()
-    app.run(host=config["HOST"], port=config["PORT"])
+    #app = get_jass_app()
+    jass_app.flask_app.run(host=config["HOST"], port=config["PORT"])
 
 
 def w_list_phenotypes(args):
diff --git a/jass/controllers/__init__.py b/jass/controllers/__init__.py
index 0e94abd..38c0339 100644
--- a/jass/controllers/__init__.py
+++ b/jass/controllers/__init__.py
@@ -7,5 +7,4 @@ Submodules
 .. autosummary::
     :toctree: _autosummary
 
-    default_controller
 """
diff --git a/jass/encoder.py b/jass/encoder.py
deleted file mode 100644
index 175502a..0000000
--- a/jass/encoder.py
+++ /dev/null
@@ -1,25 +0,0 @@
-from connexion.apps.flask_app import FlaskJSONEncoder
-
-# from connexion.decorators import produces
-from six import iteritems
-from jass.models.base_model_ import Model
-from pandas import isnull
-
-
-class JSONEncoder(FlaskJSONEncoder):
-    include_nulls = False
-
-    def default(self, o):
-        if isinstance(o, Model):
-            dikt = {}
-            for attr, _ in iteritems(o.swagger_types):
-                value = getattr(o, attr)
-                if not (isinstance(value, list)) and (value is None or isnull(value)):
-                    if not self.include_nulls:
-                        continue
-                    else:
-                        return None
-                attr = o.attribute_map[attr]
-                dikt[attr] = value
-            return dikt
-        return produces.JSONEncoder.default(self, o)
diff --git a/jass/models/project.py b/jass/models/project.py
index 86d84fd..df80a30 100644
--- a/jass/models/project.py
+++ b/jass/models/project.py
@@ -304,7 +304,8 @@ def create_project_data(
     quadrant_plot_path = None 
     ):
     
-    try:   
+    try:
+        print("TOTOOOOOO", flush=True)
         Nchunk = create_worktable_file(
                 phenotype_ids = phenotype_ids, 
                 init_file_path = init_table_path, 
diff --git a/jass/models/worktable.py b/jass/models/worktable.py
index 9728b9a..a331c7a 100644
--- a/jass/models/worktable.py
+++ b/jass/models/worktable.py
@@ -241,6 +241,8 @@ def create_worktable_file(
             This information is useful for reading the file
     :rtype: int
     """
+    
+    #return
     # number of phenotypes beyond which we change the algorithm
     K_NB_PHENOTYPES_BIG = 18
     
diff --git a/jass/server.py b/jass/server.py
index a6900af..864c44a 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -1,30 +1,306 @@
 #!/usr/bin/env python3
-"""
-Module that creates the flask app used to run JASS as a web server
-"""
-import connexion
-import flask
+import os
 
-from .encoder import JSONEncoder
-from .config import config
+from flask import Flask, redirect, send_file
+from flask.views import MethodView
+import marshmallow as ma
+from flask_smorest import Api, Blueprint, abort
+from webargs.flaskparser import FlaskParser
 
+from jass.config import config
+from jass.models.phenotype import get_available_phenotypes
+from jass.models.project import create_project, Project
 
-class JassFlaskApp(connexion.FlaskApp):
+
+class PhenotypeSchema(ma.Schema):
+    id = ma.fields.String()
+    consortium = ma.fields.String()
+    outcome = ma.fields.String()
+    full_name = ma.fields.String()
+    typ = ma.fields.String()
+    ref = ma.fields.String()
+    ref_link = ma.fields.String()
+    data_link = ma.fields.String()
+    data_path = ma.fields.String()
+
+
+class PhenotypeIdsListSchema(ma.Schema):
+    class Meta:
+        unknown = ma.EXCLUDE
+
+    phenotypeID = ma.fields.List(ma.fields.String())
+
+
+class ProjectStatusSchema(ma.Schema):
+    STATUS_VALUES = ["DOES_NOT_EXIST", "CREATING", "READY", "ERROR"]
+    global_manhattan = ma.fields.String(validate=ma.validate.OneOf(STATUS_VALUES))
+    quadrant_plot_status = ma.fields.String(validate=ma.validate.OneOf(STATUS_VALUES))
+    worktable = ma.fields.String(validate=ma.validate.OneOf(STATUS_VALUES))
+
+
+class ProjectSchema(ma.Schema):
+    id = ma.fields.String()
+    status = ma.fields.Nested(ProjectStatusSchema)
+    phenotypes = ma.fields.List(ma.fields.String())
+    progress = ma.fields.String()
+
+
+blp_phenotypes = Blueprint(
+    "phenotypes",
+    "phenotypes",
+    url_prefix="/phenotypes",
+    description="Operations on phenotypes",
+)
+
+blp_projects = Blueprint(
+    "projects", "projects", url_prefix="/projects", description="Operations on projects"
+)
+
+PHENOTYPES = get_available_phenotypes(
+    os.path.join(config["DATA_DIR"], "initTable.hdf5")
+)  # FIXME part of the config
+
+
+@blp_phenotypes.route("/")
+class PhenotypesMethodView(MethodView):
+    @blp_phenotypes.response(200, PhenotypeSchema(many=True))
+    def get(self):
+        """List phenotypes"""
+        return PHENOTYPES
+
+
+@blp_projects.route("/")
+class ProjectCreateMethodView(MethodView):
+    @blp_projects.arguments(PhenotypeIdsListSchema(), location="form")
+    @blp_projects.response(200, ProjectSchema())
+    def post(self, phenotype_ids):
+        """List projects"""
+        phenotype_ids = [
+            phenotype_id
+            for ids_with_commas in phenotype_ids["phenotypeID"]
+            for phenotype_id in ids_with_commas.split(",")
+        ]
+        phenotypes = list(filter(lambda d: d.id in phenotype_ids, PHENOTYPES))
+        return create_project([p.id for p in phenotypes], PHENOTYPES)
+
+
+@blp_projects.route("/<project_id>")
+class ProjectDetailMethodView(MethodView):
+    @blp_projects.response(200, ProjectSchema())
+    def get(self, project_id):
+        return Project(id=project_id)
+
+
+@blp_projects.route("/<project_id>/csv_status")
+class ProjectCSVStatusMethodView(MethodView):
+
+    def get(self, project_id):
+        return Project(id=project_id).get_csv_file_generation()
+
+
+@blp_projects.route("/<project_id>/summary")
+class ProjectSummaryMethodView(MethodView):
+    @blp_projects.response(200, ProjectSchema())
+    def get(self, project_id):
+        return Project(id=project_id).get_project_summary_statistics()
+
+
+@blp_projects.route("/<project_id>/genome")
+class ProjectGenomeMethodView(MethodView):
+
+    # @blp_projects.response(200, headers={"Content-Type": "text/csv"})
+    def get(self, project_id):
+        try:
+            return (
+                Project(id=project_id).get_project_genomedata(),
+                200,
+                {"Content-Type": "text/plain; charset=utf-8"},
+            )
+        except FileNotFoundError:
+            status = Project(id=project_id).status
+            if status == Project.DOES_NOT_EXIST:
+                return (
+                    f"project {project_id} does not exist",
+                    404,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+                abort(404)
+            elif status["worktable"] == Project.CREATING:
+                return (
+                    "data not ready yet",
+                    202,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            else:
+                abort(500)
+
+
+@blp_projects.route("/<project_id>/genome_full")
+class ProjectGenomeFullMethodView(MethodView):
+
+    def get(self, project_id):
+        try:
+            return send_file(
+                Project(id=project_id).get_csv_path(),
+                mimetype="text/csv",
+                as_attachment=True,
+                attachment_filename="genome_full.csv",
+            )
+        except FileNotFoundError:
+            status = Project(id=project_id).status
+            if status == Project.DOES_NOT_EXIST:
+                return (
+                    f"project {project_id} does not exist",
+                    404,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            elif status["worktable"] == Project.CREATING:
+                return (
+                    "data not ready yet",
+                    202,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            else:
+                abort(500)
+
+
+@blp_projects.route("/<project_id>/globalmanhattan")
+class ProjectGlobalManhattanMethodView(MethodView):
+
+    def get(self, project_id):
+        try:
+            return send_file(
+                Project(id=project_id).get_global_manhattan_plot_path(),
+                mimetype="image/png",
+            )
+        except FileNotFoundError:
+            status = Project(id=project_id).status
+            if status == Project.DOES_NOT_EXIST:
+                return (
+                    f"project {project_id} does not exist",
+                    404,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            elif status["global_manhattan"] == Project.CREATING:
+                return (
+                    "data not ready yet",
+                    202,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            else:
+                abort(500)
+
+
+@blp_projects.route("/<project_id>/quadrant")
+class ProjectQuadrantMethodView(MethodView):
+
+    def get(self, project_id):
+        try:
+            return send_file(
+                Project(id=project_id).get_quadrant_plot_path(),
+                mimetype="image/png",
+            )
+        except FileNotFoundError:
+            status = Project(id=project_id).status
+            if status == Project.DOES_NOT_EXIST:
+                return (
+                    f"project {project_id} does not exist",
+                    404,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            elif status["quadrant_plot_status"] == Project.CREATING:
+                return (
+                    "data not ready yet",
+                    202,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            else:
+                abort(500)
+
+
+@blp_projects.route("/<project_id>/manhattan/<chromosome>/<region>")
+class ProjectLocalManhattanMethodView(MethodView):
+
+    def get(self, project_id, chromosome, region):
+        try:
+            return (
+                Project(id=project_id).get_project_local_manhattan_data(
+                    chromosome, region
+                ),
+                200,
+                {"Content-Type": "text/plain; charset=utf-8"},
+            )
+        except FileNotFoundError:
+            status = Project(id=project_id).status
+            if status == Project.DOES_NOT_EXIST:
+                return (
+                    f"project {project_id} does not exist",
+                    404,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            elif status["worktable"] == Project.CREATING:
+                return (
+                    "data not ready yet",
+                    202,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            else:
+                abort(500)
+
+
+@blp_projects.route("/<project_id>/heatmap/<chromosome>/<region>")
+class ProjectLocalHeatMapMethodView(MethodView):
+
+    def get(self, project_id, chromosome, region):
+        try:
+            return (
+                Project(id=project_id).get_project_local_heatmap_data(
+                    chromosome, region
+                ),
+                200,
+                {"Content-Type": "text/plain; charset=utf-8"},
+            )
+        except FileNotFoundError:
+            status = Project(id=project_id).status
+            if status == Project.DOES_NOT_EXIST:
+                return (
+                    f"project {project_id} does not exist",
+                    404,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            elif status["worktable"] == Project.CREATING:
+                return (
+                    "data not ready yet",
+                    202,
+                    {"Content-Type": "text/plain; charset=utf-8"},
+                )
+            else:
+                abort(500)
+
+
+class JassApp(object):
     """
-    JassFlaskApp subclasses connexion's FlaskApp only to customize the static url path
+    JassApp builds the JASS Flask application
     """
 
+    def __init__(self):
+        self.flask_app = Flask(__name__, static_url_path="", static_folder="static")
+        self.flask_app.config["API_TITLE"] = "JASS API"
+        self.flask_app.config["API_VERSION"] = "v2.0"
+        self.flask_app.config["OPENAPI_VERSION"] = "3.0.2"
+        self.flask_app.route("/")(self.redirect_to_index)
+        self.api = Api(self.flask_app)
+
     def create_app(self):
-        app = flask.Flask(self.import_name, static_url_path="", static_folder="static")
-        app.json_encoder = JSONEncoder
-        app.route("/")(self.redirect_to_index)
-        return app
+        return self.flask_app
 
     def redirect_to_index(self):
-        return flask.redirect("index.html")
+        return redirect("index.html")
+
+    def register_api_blueprint(self, blp):
+        self.api.register_blueprint(blp, url_prefix=f"/api/{blp.url_prefix}")
 
 
-def get_jass_app():
-    app = JassFlaskApp(__name__, specification_dir="./swagger/")
-    app.add_api("swagger.yaml", arguments={"title": "JASS"}, base_path="/api")
-    return app
+jass_app = JassApp()
+jass_app.register_api_blueprint(blp_phenotypes)
+jass_app.register_api_blueprint(blp_projects)
diff --git a/jass/swagger/swagger.yaml b/jass/swagger/swagger.yaml
index c47461d..cf0b67d 100644
--- a/jass/swagger/swagger.yaml
+++ b/jass/swagger/swagger.yaml
@@ -35,7 +35,6 @@ paths:
                   "ref": "Okada et al. 2014"
                   "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/24390342"
                   "type": "Immunity"
-      x-openapi-router-controller: jass.controllers.default_controller
   /projects:
     post:
       description: |
@@ -117,7 +116,6 @@ paths:
                         "worktable": "READY"
                     progress":
                         "progress": "100"
-      x-openapi-router-controller: jass.controllers.default_controller
   "/projects/{projectID}":
     get:
       description: |
@@ -146,7 +144,6 @@ paths:
                     "worktable": "READY"
                 progress":
                     "progress": "100"
-      x-openapi-router-controller: jass.controllers.default_controller
   "/projects/{projectID}/summary":
     get:
       description: Retrieve summary statistics for a given project
@@ -174,8 +171,6 @@ paths:
                 "NoJOSTSignif":
                   "NoPhenoSignif": 1470
                   "PhenoSignif": 14
-      x-openapi-router-controller: jass.controllers.default_controller
-  
   "/projects/{projectID}/csv_status":
     get:
       description: |
@@ -200,8 +195,6 @@ paths:
                 title: csv_file_generation
               example: |
                 READY
-      x-openapi-router-controller: jass.controllers.default_controller
-  
   "/projects/{projectID}/genome":
     get:
       description: |
@@ -234,8 +227,6 @@ paths:
                 Region5,6580614.0,rs2986741,chr1,6548774,G,A,0.0013472918321710914,0.0011119999999999993,None,-3.260540717377886,2.726551316504396
                 Region6,8306267.0,rs79412885,chr1,9241839,A,G,2.0889091093474285e-13,8.106999999999937e-14,Both,7.46857160133221,-1.2003588580308502
                 Region7,10086091.5,rs113829298,chr1,10061038,T,C,4.3158209846991565e-05,6.135999999999996e-06,None,-4.5216481219798474,0.5100734569685951
-      x-openapi-router-controller: jass.controllers.default_controller
-  
   "/projects/{projectID}/genome_full":
     get:
       description: |
@@ -275,7 +266,6 @@ paths:
                 4841,1,1,rs10907190,1773772,A,G,951595.0,0.12979175667585227,0.07999999999999982,0.15999999999999964,,-0.938281041511616,1.7506860712521708
                 4842,1,1,rs10907193,1805391,A,G,951595.0,0.09562672355608258,0.06299999999999988,0.12599999999999975,,-1.0405165049626888,1.8591914944718688
                 4843,1,1,rs10907194,1712230,T,C,951595.0,0.2669995168398967,0.16000000000000425,0.3200000000000085,,-0.7600913211933399,1.4050715603096189
-      x-openapi-router-controller: jass.controllers.default_controller
   "/projects/{projectID}/globalmanhattan":
     get:
       description: |
@@ -300,7 +290,6 @@ paths:
                 title: Global manhattan plot
               example:
                 externalValue: 'globalmanhattan_example.png'
-      x-openapi-router-controller: jass.controllers.default_controller
   "/projects/{projectID}/quadrant":
     get:
       description: |
@@ -325,7 +314,6 @@ paths:
                 title: Quadrant plot
               example:
                 externalValue: 'quadrant_example.png'
-      x-openapi-router-controller: jass.controllers.default_controller
   "/projects/{projectID}/manhattan/{chromosome}/{region}":
     get:
       description: Retrieve local manhattan data
@@ -380,7 +368,6 @@ paths:
                 Region1,chr1,725196,rs377099097,0.594983644175122
                 Region1,chr1,725389,rs375619475,0.7032290172253173
                 Region1,chr1,727841,rs116587930,0.9078685880041112
-      x-openapi-router-controller: jass.controllers.default_controller
   "/projects/{projectID}/heatmap/{chromosome}/{region}":
     get:
       description: Retrieve local heatmap data
@@ -420,7 +407,6 @@ paths:
                 ID,rs545945172,rs371628865,rs61769339,rs539032812,rs12238997,rs189800799
                 z_IHEC_MONOP,-0.3623372836601329,-0.429856541533544,-0.8457360635272954,-0.9809852811227732,-0.6936527568935886,0.4382385293216385
                 z_RA_RA,,,,,,
-      x-openapi-router-controller: jass.controllers.default_controller
 components:
   schemas:
     Phenotype:
diff --git a/jass/test/__init__.py b/jass/test/__init__.py
index 86f967d..20c8988 100644
--- a/jass/test/__init__.py
+++ b/jass/test/__init__.py
@@ -1,12 +1,11 @@
 import unittest
-from ..encoder import JSONEncoder
 import logging
 import os, shutil, tempfile
 import unittest
 
-import connexion
 import flask_testing
 
+from jass.server import jass_app
 from jass.models.inittable import create_inittable_file
 
 
@@ -20,16 +19,25 @@ class JassTestCase(unittest.TestCase):
 
 class JassFlaskTestCase(JassTestCase, flask_testing.TestCase):
     def create_app(self):
-        logging.getLogger("connexion.operation").setLevel("ERROR")
         from jass.config import config
 
         self.test_dir = tempfile.mkdtemp()
         config["DATA_DIR"] = self.test_dir
         shutil.copy(self.get_file_path_fn("initTable.hdf5"), self.test_dir)
-        app = connexion.App(__name__, specification_dir="../swagger/")
-        app.app.json_encoder = JSONEncoder
-        app.add_api("swagger.yaml")
-        return app.app
+
+        self.jass_app = jass_app
+        application = self.jass_app.create_app()
+        application.config['TESTING'] = True
+
+        # Flask provides a way to test your application by exposing the Werkzeug test Client
+        # and handling the context locals for you.
+        self.testing_client = application.test_client()
+
+        # Establish an application context before running the tests.
+        #ctx = application.app_context()
+        #ctx.push()
+        #ctx.pop()
+        return application
 
     def tearDown(self):
         shutil.rmtree(self.test_dir)
diff --git a/jass/test/test_default_controller.py b/jass/test/test_server.py
similarity index 52%
rename from jass/test/test_default_controller.py
rename to jass/test/test_server.py
index 839f483..931d74d 100644
--- a/jass/test/test_default_controller.py
+++ b/jass/test/test_server.py
@@ -4,7 +4,7 @@ from __future__ import absolute_import
 import os, shutil, tempfile
 
 from six import BytesIO
-from flask import json
+from flask import json, url_for
 
 from jass.config import config
 from . import JassFlaskTestCase
@@ -17,11 +17,16 @@ class TestDefaultController(JassFlaskTestCase):
 
     def test_phenotypes_get(self):
         """
-        Test case for phenotypes_get
+        Test case retrieving available phenotypes        
+        """
+        response = self.client.open("/api/phenotypes/", method="GET")
+        self.assert200(response, "Response body is : " + response.data.decode("utf-8"))
 
-        
+    def test_create_project(self):
+        """
+        Test case for creating a project        
         """
-        response = self.client.open("/phenotypes", method="GET")
+        response = self.client.open("/api/projects/", method="POST",data={"phenotypeID":"z_IHEC_MONOP,z_RA_RA"})
         self.assert200(response, "Response body is : " + response.data.decode("utf-8"))
 
 
diff --git a/requirements.txt b/requirements.txt
index 25400d9..f6fc215 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-git+https://github.com/hmenager/connexion.git@master#egg=connexion[swagger-ui]
+flask-smorest
 aiohttp
 python_dateutil
 setuptools
diff --git a/setup.py b/setup.py
index 19675e5..67e274e 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,7 @@ README = os.path.join(SETUP_DIR, 'README.md')
 readme = open(README).read()
 
 REQUIRES = [
-    "connexion[swagger-ui] @ git+https://github.com/hmenager/connexion.git@master#egg=connexion[swagger-ui]",
+    "flask-smorest",
     "aiohttp",
     "python_dateutil",
     "setuptools",
-- 
GitLab


From a8d88801d879409fb46cf339982658fd42d8fcaf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Sat, 19 Jun 2021 22:11:44 +0200
Subject: [PATCH 10/25] remove unused connexion controller

---
 jass/controllers/default_controller.py | 172 -------------------------
 1 file changed, 172 deletions(-)
 delete mode 100644 jass/controllers/default_controller.py

diff --git a/jass/controllers/default_controller.py b/jass/controllers/default_controller.py
deleted file mode 100644
index f447e63..0000000
--- a/jass/controllers/default_controller.py
+++ /dev/null
@@ -1,172 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""
-default_controller ensures the connection between the web interface and the Python JASS-analysis module
-"""
-
-from jass.config import config
-from jass.models.project import Project, create_project
-from jass.models.phenotype import Phenotype, get_available_phenotypes
-import connexion
-from flask import send_file, abort
-from six import iteritems
-import os
-from typing import List, Dict
-
-PHENOTYPES = get_available_phenotypes(
-    os.path.join(config["DATA_DIR"], "initTable.hdf5")
-)  # FIXME part of the config
-
-
-def phenotypes_get():
-    """
-    phenotypes_get
-    Gets the list of available phenotypes 
-
-    :rtype: List[Phenotype]
-    """
-    return PHENOTYPES
-
-
-def projects_post(phenotypeID):
-    """
-    projects_post
-    Create a new project from a selection of phenotypes 
-    :param phenotypeID: IDs of the phenotypes selected for the project
-    :type phenotypeID: List[str]
-
-    :rtype: str
-    """
-    return create_project(phenotypeID, PHENOTYPES)
-
-
-def projects_project_id_csv_status_get(projectID):
-    """
-    projects_project_id_csv_status_get
-    Retrieve the generation status of the genome full csv file 
-    :param projectID: project ID
-    :type projectID: str
-
-    :rtype: str
-    """
-    return Project(id=projectID).get_csv_file_generation()
-
-
-def projects_project_id_summary_statistics(projectID):
-    """
-    projects_project_id_summary_statistics
-    Retrieve project summary statistics
-    """
-    return Project(id=projectID).get_project_summary_statistics()
-
-
-def projects_project_id_genome_get(projectID, threshold=None):
-    """
-    projects_project_id_genome_get
-    Retrieve genome data for a given project 
-    :param projectID: project ID
-    :type projectID: str
-
-    :rtype: str
-    """
-    return Project(id=projectID).get_project_genomedata()
-
-
-def projects_project_id_global_manhattan_plot_get(projectID):
-    """
-    projects_project_id_global_manhattan_plot_get
-    Gets the global Manhattan plot stored in the Project folder to display it on the Web interface
-    """
-    try:
-        return send_file(
-            Project(id=projectID).get_global_manhattan_plot_path(), mimetype="image/png"
-        )
-    except FileNotFoundError:
-        status = Project(id=projectID).status
-        if status == Project.DOES_NOT_EXIST:
-            abort(404)
-        elif status["global_manhattan"] == Project.CREATING:
-            return (
-                "Plot is not ready yet",
-                202,
-                {"Content-Type": "text/plain; charset=utf-8"},
-            )
-        else:
-            abort(500)
-
-
-def projects_project_id_quadrant_plot_get(projectID):
-    """
-    projects_project_id_quadrant_plot_get
-    Gets the quadrant plot stored in the Project folder to display it on the Web interface
-    """
-    try:
-        return send_file(
-            Project(id=projectID).get_quadrant_plot_path(), mimetype="image/png"
-        )
-    except FileNotFoundError:
-        status = Project(id=projectID).status
-        if status == Project.DOES_NOT_EXIST:
-            abort(404)
-        elif status["quadrant_plot_status"] == Project.CREATING:
-            return (
-                "Plot is not ready yet",
-                202,
-                {"Content-Type": "text/plain; charset=utf-8"},
-            )
-        else:
-            abort(500)
-
-
-def projects_project_id_genome_full_get(projectID):
-    """
-    projects_project_id_genome_full_get
-    Downloads the file genome_full.csv stored in the Project folder 
-    """
-    try:
-        return send_file(
-            Project(id=projectID).get_csv_path(),
-            mimetype="text/csv",
-            as_attachment=True,
-            attachment_filename="genome_full.csv"
-        )
-    except FileNotFoundError:
-        status = Project(id=projectID).status
-        if status == Project.DOES_NOT_EXIST:
-            abort(404)
-        elif status["worktable"] == Project.CREATING:
-            return (
-                "CSV is not ready yet",
-                202,
-                {"Content-Type": "text/plain; charset=utf-8"},
-            )
-        else:
-            abort(500)
-
-
-def projects_project_id_local_manhattan_data_get(projectID, chromosome, region):
-    """
-    projects_project_id_local_manhattan_data_get
-    Return the SumStatTab dataframe of the Project for a given chromosome and region for the Manhattan plot
-    """
-    return Project(id=projectID).get_project_local_manhattan_data(chromosome, region)
-
-
-def projects_project_id_local_heatmap_data_get(projectID, chromosome, region):
-    """
-    projects_project_id_local_heatmap_data_get
-    Return the SumStatTab dataframe of the Project for a given chromosome and region for the Heatmap plot
-    """
-    return Project(id=projectID).get_project_local_heatmap_data(chromosome, region)
-
-
-def projects_project_idget(projectID):
-    """
-    projects_project_idget
-    Retrieve a project definition 
-    :param projectID: project ID
-    :type projectID: str
-
-    :rtype: Phenotype
-    """
-    return Project(id=projectID)
-- 
GitLab


From cd89f3675fbc7203fa6fa266cc70fabdc129f237 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Sat, 19 Jun 2021 22:18:05 +0200
Subject: [PATCH 11/25] load list of phenotypes dynamically

to allow changing configuration
---
 jass/server.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/jass/server.py b/jass/server.py
index 864c44a..9fd5eff 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -56,9 +56,10 @@ blp_projects = Blueprint(
     "projects", "projects", url_prefix="/projects", description="Operations on projects"
 )
 
-PHENOTYPES = get_available_phenotypes(
-    os.path.join(config["DATA_DIR"], "initTable.hdf5")
-)  # FIXME part of the config
+def get_phenotypes():
+    return get_available_phenotypes(
+        os.path.join(config["DATA_DIR"], "initTable.hdf5")
+    )
 
 
 @blp_phenotypes.route("/")
@@ -66,7 +67,7 @@ class PhenotypesMethodView(MethodView):
     @blp_phenotypes.response(200, PhenotypeSchema(many=True))
     def get(self):
         """List phenotypes"""
-        return PHENOTYPES
+        return get_phenotypes()
 
 
 @blp_projects.route("/")
@@ -80,8 +81,8 @@ class ProjectCreateMethodView(MethodView):
             for ids_with_commas in phenotype_ids["phenotypeID"]
             for phenotype_id in ids_with_commas.split(",")
         ]
-        phenotypes = list(filter(lambda d: d.id in phenotype_ids, PHENOTYPES))
-        return create_project([p.id for p in phenotypes], PHENOTYPES)
+        phenotypes = list(filter(lambda d: d.id in phenotype_ids, get_phenotypes()))
+        return create_project([p.id for p in phenotypes], get_phenotypes())
 
 
 @blp_projects.route("/<project_id>")
@@ -278,7 +279,7 @@ class ProjectLocalHeatMapMethodView(MethodView):
                 abort(500)
 
 
-class JassApp(object):
+class JassApp(Flask):
     """
     JassApp builds the JASS Flask application
     """
-- 
GitLab


From 4285fcde72b6659b4212ee75be0146201682bd0a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Sat, 19 Jun 2021 23:29:37 +0200
Subject: [PATCH 12/25] correct the name of the testing client used in unit
 tests

---
 jass/test/__init__.py    | 10 +---------
 jass/test/test_server.py |  4 ++--
 2 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/jass/test/__init__.py b/jass/test/__init__.py
index 20c8988..945233f 100644
--- a/jass/test/__init__.py
+++ b/jass/test/__init__.py
@@ -27,16 +27,8 @@ class JassFlaskTestCase(JassTestCase, flask_testing.TestCase):
 
         self.jass_app = jass_app
         application = self.jass_app.create_app()
-        application.config['TESTING'] = True
-
-        # Flask provides a way to test your application by exposing the Werkzeug test Client
-        # and handling the context locals for you.
+        application.config["TESTING"] = True
         self.testing_client = application.test_client()
-
-        # Establish an application context before running the tests.
-        #ctx = application.app_context()
-        #ctx.push()
-        #ctx.pop()
         return application
 
     def tearDown(self):
diff --git a/jass/test/test_server.py b/jass/test/test_server.py
index 931d74d..da1b771 100644
--- a/jass/test/test_server.py
+++ b/jass/test/test_server.py
@@ -19,14 +19,14 @@ class TestDefaultController(JassFlaskTestCase):
         """
         Test case retrieving available phenotypes        
         """
-        response = self.client.open("/api/phenotypes/", method="GET")
+        response = self.testing_client.open("/api/phenotypes/", method="GET")
         self.assert200(response, "Response body is : " + response.data.decode("utf-8"))
 
     def test_create_project(self):
         """
         Test case for creating a project        
         """
-        response = self.client.open("/api/projects/", method="POST",data={"phenotypeID":"z_IHEC_MONOP,z_RA_RA"})
+        response = self.testing_client.open("/api/projects/", method="POST",data={"phenotypeID":"z_IHEC_MONOP,z_RA_RA"})
         self.assert200(response, "Response body is : " + response.data.decode("utf-8"))
 
 
-- 
GitLab


From d876097a56f01317f5fada26843750754636ee38 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Sun, 20 Jun 2021 00:20:41 +0200
Subject: [PATCH 13/25] debug the fantastic unit tests for the API

---
 jass/test/__init__.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/jass/test/__init__.py b/jass/test/__init__.py
index 945233f..b607ce0 100644
--- a/jass/test/__init__.py
+++ b/jass/test/__init__.py
@@ -19,16 +19,24 @@ class JassTestCase(unittest.TestCase):
 
 class JassFlaskTestCase(JassTestCase, flask_testing.TestCase):
     def create_app(self):
+        print("create_app start")
         from jass.config import config
-
+        print("create_app # from jass.config import config")
         self.test_dir = tempfile.mkdtemp()
+        print("create_app # self.test_dir = tempfile.mkdtemp()")
         config["DATA_DIR"] = self.test_dir
+        print("create_app # config[[\"DATA_DIR\"] = self.test_dir")
         shutil.copy(self.get_file_path_fn("initTable.hdf5"), self.test_dir)
+        print("create_app # shutil.copy(self.get_file_path_fn(\"initTable.hdf5\"), self.test_dir)")
 
         self.jass_app = jass_app
+        print("create_app # self.jass_app = jass_app")
         application = self.jass_app.create_app()
+        print("create_app # self.jass_app.create_app()")
         application.config["TESTING"] = True
+        print("create_app # application.config[\"TESTING\"] = True")
         self.testing_client = application.test_client()
+        print("create_app # self.testing_client = application.test_client()")
         return application
 
     def tearDown(self):
-- 
GitLab


From e5b34c47fa0c2f71e3e2591abc2b9b3ae9f3edb6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Sun, 20 Jun 2021 21:28:00 +0200
Subject: [PATCH 14/25] fix unit tests freezing

by mocking calls to Celery delay() method.
---
 jass/test/__init__.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/jass/test/__init__.py b/jass/test/__init__.py
index b607ce0..cbe532b 100644
--- a/jass/test/__init__.py
+++ b/jass/test/__init__.py
@@ -5,6 +5,14 @@ import unittest
 
 import flask_testing
 
+
+# replace delay() method with a mock
+# which freezes calls in unit tests
+from celery.app.task import Task
+from unittest.mock import MagicMock
+Task.delay = MagicMock()
+
+
 from jass.server import jass_app
 from jass.models.inittable import create_inittable_file
 
@@ -19,24 +27,15 @@ class JassTestCase(unittest.TestCase):
 
 class JassFlaskTestCase(JassTestCase, flask_testing.TestCase):
     def create_app(self):
-        print("create_app start")
         from jass.config import config
-        print("create_app # from jass.config import config")
         self.test_dir = tempfile.mkdtemp()
-        print("create_app # self.test_dir = tempfile.mkdtemp()")
         config["DATA_DIR"] = self.test_dir
-        print("create_app # config[[\"DATA_DIR\"] = self.test_dir")
         shutil.copy(self.get_file_path_fn("initTable.hdf5"), self.test_dir)
-        print("create_app # shutil.copy(self.get_file_path_fn(\"initTable.hdf5\"), self.test_dir)")
 
         self.jass_app = jass_app
-        print("create_app # self.jass_app = jass_app")
         application = self.jass_app.create_app()
-        print("create_app # self.jass_app.create_app()")
         application.config["TESTING"] = True
-        print("create_app # application.config[\"TESTING\"] = True")
         self.testing_client = application.test_client()
-        print("create_app # self.testing_client = application.test_client()")
         return application
 
     def tearDown(self):
-- 
GitLab


From 08683cfb2d01adaedbc34b1d23815c195047a065 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Mon, 21 Jun 2021 11:31:04 +0000
Subject: [PATCH 15/25] clean up MR before merging

(thanks to @hjulienn and @cnerin for live review)
---
 jass/__main__.py         |   1 -
 jass/models/project.py   | 809 +++++++++++++++++++--------------------
 jass/models/worktable.py |   2 -
 3 files changed, 404 insertions(+), 408 deletions(-)

diff --git a/jass/__main__.py b/jass/__main__.py
index bba3a99..a10d296 100644
--- a/jass/__main__.py
+++ b/jass/__main__.py
@@ -62,7 +62,6 @@ def absolute_path_of_the_file(fileName, output_file = False):
 
 
 def serve(args):
-    #app = get_jass_app()
     jass_app.flask_app.run(host=config["HOST"], port=config["PORT"])
 
 
diff --git a/jass/models/project.py b/jass/models/project.py
index df80a30..438c4d8 100644
--- a/jass/models/project.py
+++ b/jass/models/project.py
@@ -1,405 +1,404 @@
-# -*- coding: utf-8 -*-
-"""
-compute joint statistics and generate plots for a given set of phenotypes
-"""
-from __future__ import absolute_import
-from typing import List, Dict
-import os, sys
-import shutil
-import hashlib
-import traceback
-
-from celery import Celery
-
-from jass.models.base_model_ import Model
-from jass.util import deserialize_model
-from jass.models.phenotype import Phenotype
-from jass.models.worktable import (
-    create_worktable_file,
-    get_worktable_summary,
-    get_worktable_genomedata,
-    get_worktable_local_manhattan_data,
-    get_worktable_local_heatmap_data,
-    create_genome_full_csv
-)
-from jass.models.plots import create_global_plot, create_quadrant_plot
-from jass.config import config
-
-app = Celery("tasks", broker="pyamqp://guest@localhost//")
-
-
-class Project(Model):
-
-    DOES_NOT_EXIST = "DOES_NOT_EXIST"
-
-    CREATING = "CREATING"
-
-    READY = "READY"
-
-    ERROR = "ERROR"
-
-    def __init__(self, id: str = None, phenotypes: List[Phenotype] = None):
-        """
-        Project - a project (list of phenotypes)
-
-        :param id: project ID.
-        :type id: str
-        """
-        self.swagger_types = {"id": str, 
-            "status": str, 
-            "phenotypes": List[Phenotype], 
-            "progress": str}
-
-        self.attribute_map = {
-            "id": "id",
-            "status": "status",
-            "phenotypes": "phenotypes",
-            "progress": "progress",
-        }
-
-        self._id = id
-        self._phenotypes = phenotypes
-        if self._id is None:
-            self._id = self.get_id()
-
-    @classmethod
-    def from_dict(cls, dikt) -> "Project":
-        """
-        Returns the dict as a model
-
-        :param dikt: A dict.
-        :type: dict
-        :return: The Project.
-        :rtype: Project
-        """
-        return deserialize_model(dikt, cls)
-
-    @property
-    def id(self) -> str:
-        """
-        Gets the id of this Project.
-
-        :return: The id of this Project.
-        :rtype: str
-        """
-        return self._id
-
-    @id.setter
-    def id(self, id: str):
-        """
-        Lists the id of this Project.
-
-        :param id: The id of this Project.
-        :type id: str
-        """
-
-        self._id = id
-
-    @property
-    def phenotypes(self) -> List[Phenotype]:
-        """
-        Gets the phenotypes list for this project.
-
-        :return: The phenotypes.
-        :rtype: str
-        """
-        return self._phenotypes
-
-    @phenotypes.setter
-    def cohort(self, phenotypes: List[Phenotype]):
-        """
-        Lists the phenotypes list for this project.
-
-        :param phenotypes: The phenotypes.
-        :type phenotypes: str
-        """
-
-        self._phenotypes = phenotypes
-
-    def get_folder_path(self):
-        """
-        get_folder_path
-        Gets the path of the folder where the project data are stored
-        """
-        return os.path.join(config["DATA_DIR"], "project_{}".format(self.id))
-
-    def get_worktable_path(self):
-        """
-        get_worktable_path
-        Gets the path of the file workTable.hdf5
-        """
-        return os.path.join(self.get_folder_path(), "workTable.hdf5")
-
-    def get_csv_path(self):
-        """
-        get_csv_path
-        Gets the path of the file genome_full.csv
-        """
-        return os.path.join(self.get_folder_path(), "workTable.csv")
-
-    def get_progress_path(self):
-        """
-        get_progress_path
-        Gets the path of the file containing the current progress percentage of \
-        the analysis performed within the project 
-        """
-        return os.path.join(self.get_folder_path(), "JASS_progress.txt")
-
-    def get_csv_lock_path(self):
-        """
-        get_csv_lock_path
-        Gets the path of the lock set-on when the csv file is not available yet
-        """
-        return os.path.join(self.get_folder_path(), "the_lock.txt")
-
-    def get_project_summary_statistics(self):
-        return get_worktable_summary(self.get_worktable_path())
-
-    def get_project_genomedata(self):
-        return get_worktable_genomedata(self.get_worktable_path())
-
-    def get_project_local_manhattan_data(self, chromosome: str, region: str):
-        return get_worktable_local_manhattan_data(
-            self.get_worktable_path(), chromosome, region
-        )
-
-    def get_project_local_heatmap_data(self, chromosome: str, region: str):
-        return get_worktable_local_heatmap_data(
-            self.get_worktable_path(), chromosome, region
-        )
-
-    def get_id(self):
-        m = hashlib.md5()
-        for phenotype_id in [phenotype.id for phenotype in self._phenotypes]:
-            m.update(str(phenotype_id).encode("utf-8"))
-        return m.hexdigest()
-
-    def get_global_manhattan_plot_path(self):
-        return os.path.join(self.get_folder_path(), "Manhattan_Plot_Omnibus.png")
-
-    def get_quadrant_plot_path(self):
-        return os.path.join(self.get_folder_path(), "Quadrant_Plot_Omnibus.png")
-
-    @property
-    def status(self):
-        """
-        status
-        Gets the status of the project
-        """
-        if not os.path.exists(self.get_folder_path()):
-            return Project.DOES_NOT_EXIST
-        else:
-            worktable_status = get_file_status(self.get_worktable_path())
-            global_manhattan_status = get_file_status(
-                self.get_global_manhattan_plot_path()
-            )
-            quadrant_plot_status = get_file_status(self.get_quadrant_plot_path())
-            return {
-                # WARNING: project status is hacked so that everything is ready
-                # only once the final step has completed.
-                # This avoids the apparent "corrupted hdf5" file situation
-                # "worktable": worktable_status,
-                # "global_manhattan": global_manhattan_status,
-                "worktable": quadrant_plot_status,
-                "global_manhattan": quadrant_plot_status,
-                "quadrant_plot_status": quadrant_plot_status,
-            }
-
-    @property
-    def progress(self):
-        """
-        progress
-        Gets the percentage of completion of the phenotype analysis
-        """
-        JASS_progress = 0
-        progress_path = self.get_progress_path()
-        if os.path.exists(progress_path):
-            file_progress = open(progress_path, "r")
-            JASS_progress = file_progress.read()
-            file_progress.close()
-        return JASS_progress
-
-    def get_csv_file_generation(self):
-        """
-        csv_file_generation
-        Gets the status of the genome_full csv file generation
-        """
-        the_lock_path = self.get_csv_lock_path()
-        csv_file = self.get_csv_path()
-        csv_file_status = Project.CREATING
-        if (not os.path.isfile(the_lock_path)):
-            if(os.path.isfile(csv_file)):
-                csv_file_status = Project.READY
-            else :
-                csv_file_status = Project.ERROR
-        print("csv_file_generation:csv_file_status={}".format(csv_file_status))
-        return csv_file_status
-
-def get_file_building_tb_path(file_path):
-    return file_path + ".log"
-
-
-def get_file_status(file_path):
-    if os.path.exists(file_path):
-        return Project.READY
-    elif os.path.exists(get_file_building_tb_path(file_path)):
-        return Project.ERROR
-    else:
-        return Project.CREATING
-
-
-@app.task
-def create_project_global_plot(worktable_path, plot_path):
-    try:
-        create_global_plot(worktable_path, plot_path)
-    except Exception as e:
-        exc_type, exc_value, exc_traceback = sys.exc_info()
-        log_path = get_file_building_tb_path(plot_path)
-        log_fh = open(log_path, "w")
-        traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
-        log_fh.close()
-
-
-@app.task
-def create_project_quadrant_plot(worktable_path, plot_path):
-    try:
-        create_quadrant_plot(worktable_path, plot_path)
-    except Exception as e:
-        exc_type, exc_value, exc_traceback = sys.exc_info()
-        log_path = get_file_building_tb_path(plot_path)
-        log_fh = open(log_path, "w")
-        traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
-        log_fh.close()
-
-
-@app.task
-def create_project_csv_file(worktable_path, csv_file, Nchunk):
-    try:
-        create_genome_full_csv(worktable_path, csv_file, Nchunk=Nchunk)
-    except Exception as e:
-        exc_type, exc_value, exc_traceback = sys.exc_info()
-        log_path = get_file_building_tb_path(plot_path)
-        log_fh = open(log_path, "w")
-        traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
-        log_fh.close()
-
-
-@app.task
-def create_project_data(
-    phenotype_ids, 
-    init_table_path, 
-    worktable_path,
-    remove_nan = False,
-    stat = "jass.models.stats:omnibus_stat",
-    csv_file = None,
-    chunk_size = 50,
-    significance_treshold = 5*10**-8,
-    post_filtering = True,
-    delayed_gen_csv_file = False,
-    chromosome = None,
-    start = None,
-    end = None,
-    custom_loadings = None,
-    global_plot_path = None, 
-    quadrant_plot_path = None 
-    ):
-    
-    try:
-        print("TOTOOOOOO", flush=True)
-        Nchunk = create_worktable_file(
-                phenotype_ids = phenotype_ids, 
-                init_file_path = init_table_path, 
-                project_hdf_path = worktable_path, 
-                remove_nan = remove_nan,
-                stat = stat,
-                optim_na = True,
-                csv_file = csv_file,
-                chunk_size = chunk_size,
-                significance_treshold = significance_treshold,
-                post_filtering = post_filtering,
-                delayed_gen_csv_file = delayed_gen_csv_file,
-                chromosome = chromosome,
-                pos_Start = start,
-                pos_End = end,
-                custom_loadings = custom_loadings
-                )
-    except Exception as e:
-        exc_type, exc_value, exc_traceback = sys.exc_info()
-        log_path = get_file_building_tb_path(worktable_path)
-        log_fh = open(log_path, "w")
-        traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
-        log_fh.close()
-        return
-    
-    if (global_plot_path is not None):
-        create_project_global_plot.delay(worktable_path, global_plot_path)
-    if (quadrant_plot_path is not None):
-        create_project_quadrant_plot.delay(worktable_path, quadrant_plot_path)
-    if (delayed_gen_csv_file and (csv_file is not None)):
-        create_project_csv_file.delay(worktable_path, csv_file, Nchunk=Nchunk)
-
-
-def create_project(phenotype_ids: List[str], available_phenotypes: List[Phenotype]):
-    available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
-    unavailable_requested_ids = set(phenotype_ids).difference(
-        set(available_phenotype_ids)
-    )
-    if len(unavailable_requested_ids) > 0:
-        raise Exception()  # FIXME with a nice exception
-    phenotypes = [
-        phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
-    ]
-    project = Project(phenotypes=phenotypes)
-    folder_path = project.get_folder_path()
-    # if project does not exist
-    if project.status == Project.DOES_NOT_EXIST:
-        os.makedirs(folder_path)
-        create_project_data.delay(
-            phenotype_ids=phenotype_ids,
-            init_table_path=os.path.join(config["DATA_DIR"], "initTable.hdf5"),
-            worktable_path=project.get_worktable_path(),
-            global_plot_path=project.get_global_manhattan_plot_path(),
-            quadrant_plot_path=project.get_quadrant_plot_path(),
-            csv_file=project.get_csv_path(),
-            delayed_gen_csv_file=True
-        )
-    return project
- 
- 
-def create_project_local(
-    phenotype_ids: List[str], 
-    available_phenotypes: List[Phenotype],
-    ip: str,
-    chromosome: str,
-    start: str = None,
-    end: str = None
-    ):
-    available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
-    unavailable_requested_ids = set(phenotype_ids).difference(
-        set(available_phenotype_ids)
-    )
-    if len(unavailable_requested_ids) > 0:
-        raise Exception()  # FIXME with a nice exception
-    phenotypes = [
-        phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
-    ]
-    ip = ip.replace('.', '_')
-    id_project = "local_{}".format(ip)
-    project = Project(phenotypes=phenotypes, id=id_project)
-    folder_path = project.get_folder_path()
-    # If the folder exists, it is deleted with the files it contains
-    if os.path.exists(folder_path):
-        shutil.rmtree(folder_path)
-    # The folder is created
-    os.makedirs(folder_path)
-    create_project_data.delay(
-        phenotype_ids=phenotype_ids,
-        init_table_path=os.path.join(config["DATA_DIR"], "initTable.hdf5"),
-        worktable_path=project.get_worktable_path(),
-        csv_file=project.get_csv_path(),
-        chromosome=chromosome,
-        start=start,
-        end=end
-        )
-    return project
-    
\ No newline at end of file
+# -*- coding: utf-8 -*-
+"""
+compute joint statistics and generate plots for a given set of phenotypes
+"""
+from __future__ import absolute_import
+from typing import List, Dict
+import os, sys
+import shutil
+import hashlib
+import traceback
+
+from celery import Celery
+
+from jass.models.base_model_ import Model
+from jass.util import deserialize_model
+from jass.models.phenotype import Phenotype
+from jass.models.worktable import (
+    create_worktable_file,
+    get_worktable_summary,
+    get_worktable_genomedata,
+    get_worktable_local_manhattan_data,
+    get_worktable_local_heatmap_data,
+    create_genome_full_csv
+)
+from jass.models.plots import create_global_plot, create_quadrant_plot
+from jass.config import config
+
+app = Celery("tasks", broker="pyamqp://guest@localhost//")
+
+
+class Project(Model):
+
+    DOES_NOT_EXIST = "DOES_NOT_EXIST"
+
+    CREATING = "CREATING"
+
+    READY = "READY"
+
+    ERROR = "ERROR"
+
+    def __init__(self, id: str = None, phenotypes: List[Phenotype] = None):
+        """
+        Project - a project (list of phenotypes)
+
+        :param id: project ID.
+        :type id: str
+        """
+        self.swagger_types = {"id": str, 
+            "status": str, 
+            "phenotypes": List[Phenotype], 
+            "progress": str}
+
+        self.attribute_map = {
+            "id": "id",
+            "status": "status",
+            "phenotypes": "phenotypes",
+            "progress": "progress",
+        }
+
+        self._id = id
+        self._phenotypes = phenotypes
+        if self._id is None:
+            self._id = self.get_id()
+
+    @classmethod
+    def from_dict(cls, dikt) -> "Project":
+        """
+        Returns the dict as a model
+
+        :param dikt: A dict.
+        :type: dict
+        :return: The Project.
+        :rtype: Project
+        """
+        return deserialize_model(dikt, cls)
+
+    @property
+    def id(self) -> str:
+        """
+        Gets the id of this Project.
+
+        :return: The id of this Project.
+        :rtype: str
+        """
+        return self._id
+
+    @id.setter
+    def id(self, id: str):
+        """
+        Lists the id of this Project.
+
+        :param id: The id of this Project.
+        :type id: str
+        """
+
+        self._id = id
+
+    @property
+    def phenotypes(self) -> List[Phenotype]:
+        """
+        Gets the phenotypes list for this project.
+
+        :return: The phenotypes.
+        :rtype: str
+        """
+        return self._phenotypes
+
+    @phenotypes.setter
+    def cohort(self, phenotypes: List[Phenotype]):
+        """
+        Lists the phenotypes list for this project.
+
+        :param phenotypes: The phenotypes.
+        :type phenotypes: str
+        """
+
+        self._phenotypes = phenotypes
+
+    def get_folder_path(self):
+        """
+        get_folder_path
+        Gets the path of the folder where the project data are stored
+        """
+        return os.path.join(config["DATA_DIR"], "project_{}".format(self.id))
+
+    def get_worktable_path(self):
+        """
+        get_worktable_path
+        Gets the path of the file workTable.hdf5
+        """
+        return os.path.join(self.get_folder_path(), "workTable.hdf5")
+
+    def get_csv_path(self):
+        """
+        get_csv_path
+        Gets the path of the file genome_full.csv
+        """
+        return os.path.join(self.get_folder_path(), "workTable.csv")
+
+    def get_progress_path(self):
+        """
+        get_progress_path
+        Gets the path of the file containing the current progress percentage of \
+        the analysis performed within the project 
+        """
+        return os.path.join(self.get_folder_path(), "JASS_progress.txt")
+
+    def get_csv_lock_path(self):
+        """
+        get_csv_lock_path
+        Gets the path of the lock set-on when the csv file is not available yet
+        """
+        return os.path.join(self.get_folder_path(), "the_lock.txt")
+
+    def get_project_summary_statistics(self):
+        return get_worktable_summary(self.get_worktable_path())
+
+    def get_project_genomedata(self):
+        return get_worktable_genomedata(self.get_worktable_path())
+
+    def get_project_local_manhattan_data(self, chromosome: str, region: str):
+        return get_worktable_local_manhattan_data(
+            self.get_worktable_path(), chromosome, region
+        )
+
+    def get_project_local_heatmap_data(self, chromosome: str, region: str):
+        return get_worktable_local_heatmap_data(
+            self.get_worktable_path(), chromosome, region
+        )
+
+    def get_id(self):
+        m = hashlib.md5()
+        for phenotype_id in [phenotype.id for phenotype in self._phenotypes]:
+            m.update(str(phenotype_id).encode("utf-8"))
+        return m.hexdigest()
+
+    def get_global_manhattan_plot_path(self):
+        return os.path.join(self.get_folder_path(), "Manhattan_Plot_Omnibus.png")
+
+    def get_quadrant_plot_path(self):
+        return os.path.join(self.get_folder_path(), "Quadrant_Plot_Omnibus.png")
+
+    @property
+    def status(self):
+        """
+        status
+        Gets the status of the project
+        """
+        if not os.path.exists(self.get_folder_path()):
+            return Project.DOES_NOT_EXIST
+        else:
+            worktable_status = get_file_status(self.get_worktable_path())
+            global_manhattan_status = get_file_status(
+                self.get_global_manhattan_plot_path()
+            )
+            quadrant_plot_status = get_file_status(self.get_quadrant_plot_path())
+            return {
+                # WARNING: project status is hacked so that everything is ready
+                # only once the final step has completed.
+                # This avoids the apparent "corrupted hdf5" file situation
+                # "worktable": worktable_status,
+                # "global_manhattan": global_manhattan_status,
+                "worktable": quadrant_plot_status,
+                "global_manhattan": quadrant_plot_status,
+                "quadrant_plot_status": quadrant_plot_status,
+            }
+
+    @property
+    def progress(self):
+        """
+        progress
+        Gets the percentage of completion of the phenotype analysis
+        """
+        JASS_progress = 0
+        progress_path = self.get_progress_path()
+        if os.path.exists(progress_path):
+            file_progress = open(progress_path, "r")
+            JASS_progress = file_progress.read()
+            file_progress.close()
+        return JASS_progress
+
+    def get_csv_file_generation(self):
+        """
+        csv_file_generation
+        Gets the status of the genome_full csv file generation
+        """
+        the_lock_path = self.get_csv_lock_path()
+        csv_file = self.get_csv_path()
+        csv_file_status = Project.CREATING
+        if (not os.path.isfile(the_lock_path)):
+            if(os.path.isfile(csv_file)):
+                csv_file_status = Project.READY
+            else :
+                csv_file_status = Project.ERROR
+        print("csv_file_generation:csv_file_status={}".format(csv_file_status))
+        return csv_file_status
+
+def get_file_building_tb_path(file_path):
+    return file_path + ".log"
+
+
+def get_file_status(file_path):
+    if os.path.exists(file_path):
+        return Project.READY
+    elif os.path.exists(get_file_building_tb_path(file_path)):
+        return Project.ERROR
+    else:
+        return Project.CREATING
+
+
+@app.task
+def create_project_global_plot(worktable_path, plot_path):
+    try:
+        create_global_plot(worktable_path, plot_path)
+    except Exception as e:
+        exc_type, exc_value, exc_traceback = sys.exc_info()
+        log_path = get_file_building_tb_path(plot_path)
+        log_fh = open(log_path, "w")
+        traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
+        log_fh.close()
+
+
+@app.task
+def create_project_quadrant_plot(worktable_path, plot_path):
+    try:
+        create_quadrant_plot(worktable_path, plot_path)
+    except Exception as e:
+        exc_type, exc_value, exc_traceback = sys.exc_info()
+        log_path = get_file_building_tb_path(plot_path)
+        log_fh = open(log_path, "w")
+        traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
+        log_fh.close()
+
+
+@app.task
+def create_project_csv_file(worktable_path, csv_file, Nchunk):
+    try:
+        create_genome_full_csv(worktable_path, csv_file, Nchunk=Nchunk)
+    except Exception as e:
+        exc_type, exc_value, exc_traceback = sys.exc_info()
+        log_path = get_file_building_tb_path(plot_path)
+        log_fh = open(log_path, "w")
+        traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
+        log_fh.close()
+
+
+@app.task
+def create_project_data(
+    phenotype_ids, 
+    init_table_path, 
+    worktable_path,
+    remove_nan = False,
+    stat = "jass.models.stats:omnibus_stat",
+    csv_file = None,
+    chunk_size = 50,
+    significance_treshold = 5*10**-8,
+    post_filtering = True,
+    delayed_gen_csv_file = False,
+    chromosome = None,
+    start = None,
+    end = None,
+    custom_loadings = None,
+    global_plot_path = None, 
+    quadrant_plot_path = None 
+    ):
+    
+    try:   
+        Nchunk = create_worktable_file(
+                phenotype_ids = phenotype_ids, 
+                init_file_path = init_table_path, 
+                project_hdf_path = worktable_path, 
+                remove_nan = remove_nan,
+                stat = stat,
+                optim_na = True,
+                csv_file = csv_file,
+                chunk_size = chunk_size,
+                significance_treshold = significance_treshold,
+                post_filtering = post_filtering,
+                delayed_gen_csv_file = delayed_gen_csv_file,
+                chromosome = chromosome,
+                pos_Start = start,
+                pos_End = end,
+                custom_loadings = custom_loadings
+                )
+    except Exception as e:
+        exc_type, exc_value, exc_traceback = sys.exc_info()
+        log_path = get_file_building_tb_path(worktable_path)
+        log_fh = open(log_path, "w")
+        traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
+        log_fh.close()
+        return
+    
+    if (global_plot_path is not None):
+        create_project_global_plot.delay(worktable_path, global_plot_path)
+    if (quadrant_plot_path is not None):
+        create_project_quadrant_plot.delay(worktable_path, quadrant_plot_path)
+    if (delayed_gen_csv_file and (csv_file is not None)):
+        create_project_csv_file.delay(worktable_path, csv_file, Nchunk=Nchunk)
+
+
+def create_project(phenotype_ids: List[str], available_phenotypes: List[Phenotype]):
+    available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
+    unavailable_requested_ids = set(phenotype_ids).difference(
+        set(available_phenotype_ids)
+    )
+    if len(unavailable_requested_ids) > 0:
+        raise Exception()  # FIXME with a nice exception
+    phenotypes = [
+        phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
+    ]
+    project = Project(phenotypes=phenotypes)
+    folder_path = project.get_folder_path()
+    # if project does not exist
+    if project.status == Project.DOES_NOT_EXIST:
+        os.makedirs(folder_path)
+        create_project_data.delay(
+            phenotype_ids=phenotype_ids,
+            init_table_path=os.path.join(config["DATA_DIR"], "initTable.hdf5"),
+            worktable_path=project.get_worktable_path(),
+            global_plot_path=project.get_global_manhattan_plot_path(),
+            quadrant_plot_path=project.get_quadrant_plot_path(),
+            csv_file=project.get_csv_path(),
+            delayed_gen_csv_file=True
+        )
+    return project
+ 
+ 
+def create_project_local(
+    phenotype_ids: List[str], 
+    available_phenotypes: List[Phenotype],
+    ip: str,
+    chromosome: str,
+    start: str = None,
+    end: str = None
+    ):
+    available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
+    unavailable_requested_ids = set(phenotype_ids).difference(
+        set(available_phenotype_ids)
+    )
+    if len(unavailable_requested_ids) > 0:
+        raise Exception()  # FIXME with a nice exception
+    phenotypes = [
+        phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
+    ]
+    ip = ip.replace('.', '_')
+    id_project = "local_{}".format(ip)
+    project = Project(phenotypes=phenotypes, id=id_project)
+    folder_path = project.get_folder_path()
+    # If the folder exists, it is deleted with the files it contains
+    if os.path.exists(folder_path):
+        shutil.rmtree(folder_path)
+    # The folder is created
+    os.makedirs(folder_path)
+    create_project_data.delay(
+        phenotype_ids=phenotype_ids,
+        init_table_path=os.path.join(config["DATA_DIR"], "initTable.hdf5"),
+        worktable_path=project.get_worktable_path(),
+        csv_file=project.get_csv_path(),
+        chromosome=chromosome,
+        start=start,
+        end=end
+        )
+    return project
+    
diff --git a/jass/models/worktable.py b/jass/models/worktable.py
index a331c7a..9728b9a 100644
--- a/jass/models/worktable.py
+++ b/jass/models/worktable.py
@@ -241,8 +241,6 @@ def create_worktable_file(
             This information is useful for reading the file
     :rtype: int
     """
-    
-    #return
     # number of phenotypes beyond which we change the algorithm
     K_NB_PHENOTYPES_BIG = 18
     
-- 
GitLab


From c7e03f27ba7a22634a5dfcf760b458dc8d171e51 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Thu, 8 Jul 2021 09:37:04 +0200
Subject: [PATCH 16/25] add mocking celery's delay for unit tests

---
 jass/test/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/jass/test/__init__.py b/jass/test/__init__.py
index cbe532b..8f9a6a1 100644
--- a/jass/test/__init__.py
+++ b/jass/test/__init__.py
@@ -3,6 +3,7 @@ import logging
 import os, shutil, tempfile
 import unittest
 
+
 import flask_testing
 
 
-- 
GitLab


From 2ec52fcc5df3ea1333d3e86b394f3fce4e70a5b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Thu, 8 Jul 2021 13:44:36 +0200
Subject: [PATCH 17/25] replace Task.si() method with a MagicMock

...to avoid freezing calls in unit tests
---
 jass/test/__init__.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/jass/test/__init__.py b/jass/test/__init__.py
index 8f9a6a1..7ddc6ba 100644
--- a/jass/test/__init__.py
+++ b/jass/test/__init__.py
@@ -7,12 +7,12 @@ import unittest
 import flask_testing
 
 
-# replace delay() method with a mock
-# which freezes calls in unit tests
+# replace delay() and si() method with mocks
+# to avoid freezing calls in unit tests
 from celery.app.task import Task
 from unittest.mock import MagicMock
 Task.delay = MagicMock()
-
+Task.si = MagicMock()
 
 from jass.server import jass_app
 from jass.models.inittable import create_inittable_file
-- 
GitLab


From 9c77cba966803e1812774e8f1cb7e016b84ad373 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Thu, 8 Jul 2021 14:27:59 +0200
Subject: [PATCH 18/25] reformat source with black

---
 jass/__init__.py             |   2 +-
 jass/celeryconfig.py         |  14 +-
 jass/models/inittable.py     | 181 +++++++------
 jass/models/project.py       |   9 +-
 jass/models/stats.py         |  46 ++--
 jass/models/worktable.py     | 512 +++++++++++++++++++++++------------
 jass/server.py               |   1 -
 jass/tasks.py                | 220 +++++++--------
 jass/test/__init__.py        |   2 +
 jass/test/test_init_table.py |  10 +-
 jass/test/test_plots.py      |   1 +
 jass/test/test_server.py     |  12 +-
 jass/test/test_worktable.py  |  17 +-
 jass/util.py                 |  16 +-
 14 files changed, 628 insertions(+), 415 deletions(-)

diff --git a/jass/__init__.py b/jass/__init__.py
index e27073c..a88eb7a 100644
--- a/jass/__init__.py
+++ b/jass/__init__.py
@@ -17,4 +17,4 @@ Submodules
 """
 import os
 
-from jass.tasks import celery
\ No newline at end of file
+from jass.tasks import celery
diff --git a/jass/celeryconfig.py b/jass/celeryconfig.py
index 2350b9a..1530851 100644
--- a/jass/celeryconfig.py
+++ b/jass/celeryconfig.py
@@ -1,17 +1,15 @@
 import os
 
 ## Broker settings.
-broker_url = os.getenv('JASS_RABBITMQ_URL','amqp://guest:guest@localhost:5672//')
+broker_url = os.getenv("JASS_RABBITMQ_URL", "amqp://guest:guest@localhost:5672//")
 
 ## Broker settings.
-#result_backend = os.getenv('JASS_RABBITMQ_URL','amqp://guest2:guest@localhost:5672//')
-result_backend='rpc://'
+# result_backend = os.getenv('JASS_RABBITMQ_URL','amqp://guest2:guest@localhost:5672//')
+result_backend = "rpc://"
 # List of modules to import when the Celery worker starts.
-#imports = ('myapp.tasks',)
+# imports = ('myapp.tasks',)
 
 ## Using the database to store task state and results.
-#result_backend = 'db+sqlite:///results.db'
-
-#task_annotations = {'tasks.add': {'rate_limit': '10/s'}}
-
+# result_backend = 'db+sqlite:///results.db'
 
+# task_annotations = {'tasks.add': {'rate_limit': '10/s'}}
diff --git a/jass/models/inittable.py b/jass/models/inittable.py
index 15fcd0f..7a2849d 100644
--- a/jass/models/inittable.py
+++ b/jass/models/inittable.py
@@ -18,6 +18,7 @@ from functools import reduce
 options.mode.chained_assignment = None
 warnings.filterwarnings("ignore", category=tables.NaturalNameWarning)
 
+
 def get_gwasname(file_name):
     return "_".join(os.path.basename(file_name).split("_")[0:3])
 
@@ -33,9 +34,9 @@ def check_if_SNP_unique(z_gwas_chrom):
 
 def get_gwas_dict(input_data_path):
     gwas_dict = {}
-    #retrieve all files corresponding to glob patterns
+    # retrieve all files corresponding to glob patterns
     files_by_pattern = list(map(glob.glob, input_data_path.split(";")))
-    all_path = reduce(lambda x,y:x+y, files_by_pattern)
+    all_path = reduce(lambda x, y: x + y, files_by_pattern)
     print(all_path)
     for x in all_path:
         gwas_name = get_gwasname(x)
@@ -60,17 +61,27 @@ def create_pheno_summary(description):
             "internalDataLink",
             "Nsample",
             "Ncase",
-            "Ncontrol"
+            "Ncontrol",
         ]
     ]
 
-    pheno_summary_data["ID"] =  "z_" + pheno_summary_data.Consortium.str.upper() + "_" + pheno_summary_data.Outcome.str.upper()
+    pheno_summary_data["ID"] = (
+        "z_"
+        + pheno_summary_data.Consortium.str.upper()
+        + "_"
+        + pheno_summary_data.Outcome.str.upper()
+    )
 
-    is_quantitatif = pheno_summary_data['Ncase'].isnull()
+    is_quantitatif = pheno_summary_data["Ncase"].isnull()
     pheno_summary_data["Effective_sample_size"] = np.nan
-    pheno_summary_data.loc[~is_quantitatif,"Effective_sample_size"] = (pheno_summary_data.loc[~is_quantitatif, "Ncase"]*pheno_summary_data.loc[~is_quantitatif, "Ncontrol"]) / pheno_summary_data.loc[~is_quantitatif, "Nsample"]
+    pheno_summary_data.loc[~is_quantitatif, "Effective_sample_size"] = (
+        pheno_summary_data.loc[~is_quantitatif, "Ncase"]
+        * pheno_summary_data.loc[~is_quantitatif, "Ncontrol"]
+    ) / pheno_summary_data.loc[~is_quantitatif, "Nsample"]
 
-    pheno_summary_data.loc[is_quantitatif,"Effective_sample_size"] = pheno_summary_data.loc[is_quantitatif, "Nsample"]
+    pheno_summary_data.loc[
+        is_quantitatif, "Effective_sample_size"
+    ] = pheno_summary_data.loc[is_quantitatif, "Nsample"]
 
     # reorder columns in the dataframe
     pheno_summary_data = pheno_summary_data[
@@ -87,7 +98,7 @@ def create_pheno_summary(description):
             "Nsample",
             "Ncase",
             "Ncontrol",
-            "Effective_sample_size"
+            "Effective_sample_size",
         ]
     ]
     pheno_summary_data.index = pheno_summary_data["ID"]
@@ -121,21 +132,23 @@ def format_chr_gwas(gwas_file_chri, chrom, study_name, regions_bychr):
     z_gwas["Region"] = 0
     z_gwas["MiddlePosition"] = 0.0
 
-    for region_index, region_row in regions_bychr.get_group(
-        "chr%d" % chrom
-    ).iterrows():
+    for region_index, region_row in regions_bychr.get_group("chr%d" % chrom).iterrows():
         left = region_row["start"]
         right = region_row["stop"]
         ind = (z_gwas["position"] >= left) & (z_gwas["position"] <= right)
         (z_gwas.loc[ind, "Region"]) = np.int(region_index + 1)
         (z_gwas.loc[ind, "MiddlePosition"]) = (left + right) / 2
-    return(z_gwas)
+    return z_gwas
 
 
 def compute_covariance_zscore(init_file_path):
     print("## Compute covariance ##")
-    sum_stat_jost_tab = read_hdf(init_file_path, 'SumStatTab', where='Region >= {0} and Region < {1}'.format(0, 3))
-    trait = [i for i in sum_stat_jost_tab.columns if i[:2]=="z_"]
+    sum_stat_jost_tab = read_hdf(
+        init_file_path,
+        "SumStatTab",
+        where="Region >= {0} and Region < {1}".format(0, 3),
+    )
+    trait = [i for i in sum_stat_jost_tab.columns if i[:2] == "z_"]
 
     NSNP_matrix = DataFrame(index=trait, columns=trait)
     cov_matrix = DataFrame(index=trait, columns=trait)
@@ -143,31 +156,35 @@ def compute_covariance_zscore(init_file_path):
     cov_matrix.fillna(0, inplace=True)
     NSNP_matrix.fillna(0, inplace=True)
 
-    bi = range(0,1751,50)
-    n_len = len(bi)-1
+    bi = range(0, 1751, 50)
+    n_len = len(bi) - 1
 
     for i in range(n_len):
         binf = bi[i]
-        bsup = bi[(i+1)]
-        sum_stat_jost_tab = read_hdf(init_file_path, 'SumStatTab', where='Region >= {0} and Region < {1}'.format(binf, bsup))
+        bsup = bi[(i + 1)]
+        sum_stat_jost_tab = read_hdf(
+            init_file_path,
+            "SumStatTab",
+            where="Region >= {0} and Region < {1}".format(binf, bsup),
+        )
 
         print("Regions {0} to {1}\r".format(binf, bsup))
         j = 0
         for tr1 in trait:
             for tr2 in trait[j:]:
-                cc = sum_stat_jost_tab[[tr1,tr2]].dropna()
+                cc = sum_stat_jost_tab[[tr1, tr2]].dropna()
                 cc = cc.loc[cc.max(1) < 4]
 
-                cov_matrix.loc[tr1,tr2] += cc.iloc[:,0].dot(cc.iloc[:,1])
-                NSNP_matrix.loc[tr1,tr2] += cc.shape[0]
+                cov_matrix.loc[tr1, tr2] += cc.iloc[:, 0].dot(cc.iloc[:, 1])
+                NSNP_matrix.loc[tr1, tr2] += cc.shape[0]
 
-                cov_matrix.loc[tr2,tr1] += cc.iloc[:,0].dot(cc.iloc[:,1])
-                NSNP_matrix.loc[tr2,tr1] += cc.shape[0]
-            j=j+1
+                cov_matrix.loc[tr2, tr1] += cc.iloc[:, 0].dot(cc.iloc[:, 1])
+                NSNP_matrix.loc[tr2, tr1] += cc.shape[0]
+            j = j + 1
 
-    #(cov_matrix/NSNP_matrix).to_csv("Covariance_on_Zscores.csv", sep="\t")
+    # (cov_matrix/NSNP_matrix).to_csv("Covariance_on_Zscores.csv", sep="\t")
     hdf_init = HDFStore(init_file_path)
-    hdf_init.put("COV", (cov_matrix/NSNP_matrix), format="table", data_columns=True)
+    hdf_init.put("COV", (cov_matrix / NSNP_matrix), format="table", data_columns=True)
     hdf_init.close()
 
 
@@ -177,18 +194,20 @@ def create_inittable_file(
     description_file_path: str,
     init_table_path: str,
     init_covariance_path=None,
-    init_genetic_covariance_path=None
+    init_genetic_covariance_path=None,
 ):
     # Read region file
-    regions = read_csv(regions_map_path, sep='\s+', memory_map=True)
+    regions = read_csv(regions_map_path, sep="\s+", memory_map=True)
     # Create HDFStore
     if os.path.exists(init_table_path):
         os.remove(init_table_path)
     hdf_init = HDFStore(init_table_path)
 
     # Read covariance file
-    if init_covariance_path!=None:
-        covariance = read_csv(init_covariance_path, sep="\t", index_col=0, memory_map=True)
+    if init_covariance_path != None:
+        covariance = read_csv(
+            init_covariance_path, sep="\t", index_col=0, memory_map=True
+        )
         compute_covariance = False
     else:
         compute_covariance = True
@@ -206,18 +225,20 @@ def create_inittable_file(
             "z_" + meta_row["Consortium"].upper() + "_" + meta_row["Outcome"].upper()
         )
 
-    pheno_select = list(phenotypes_list) & gwas_dict.keys() #&covariance.columns
+    pheno_select = list(phenotypes_list) & gwas_dict.keys()  # &covariance.columns
     pheno_summary_data = create_pheno_summary(description)
 
     # select only phenotypes for which there is a covariance
     pheno_list = pheno_summary_data.loc[pheno_select, :]
-    if compute_covariance==False:
+    if compute_covariance == False:
         COV = covariance.loc[pheno_select, pheno_select]
         hdf_init.put("COV", COV, format="table", data_columns=True)
 
     # Read Genetic Covariance file and add genetic correlation if available
-    if init_genetic_covariance_path!=None:
-        genetic_covariance = read_csv(init_genetic_covariance_path, sep="\t", index_col=0, memory_map=True)
+    if init_genetic_covariance_path != None:
+        genetic_covariance = read_csv(
+            init_genetic_covariance_path, sep="\t", index_col=0, memory_map=True
+        )
         GEN_COV = genetic_covariance.loc[pheno_select, pheno_select]
         hdf_init.put("GEN_COV", GEN_COV, format="table", data_columns=True)
 
@@ -234,7 +255,7 @@ def create_inittable_file(
     which_cols.extend(list(pheno_select))
     hdf_init.put("PhenoList", pheno_list, format="table", data_columns=True)
     hdf_init.put("Regions", regions, format="table", data_columns=True)
-    sum_stat_tab_min_itemsizes = {"snp_ids": 80, "Ref_allele":70,"Alt_allele":70}
+    sum_stat_tab_min_itemsizes = {"snp_ids": 80, "Ref_allele": 70, "Alt_allele": 70}
 
     regions_bychr = regions.groupby("chr")
 
@@ -326,16 +347,15 @@ def create_inittable_file(
         compute_covariance_zscore(init_table_path)
 
 
-def add_gene_annotation(gene_data_path, 
-                        initTable_path=None, 
-                        df_gene_csv_path=None, 
-                        df_exon_csv_path=None):
+def add_gene_annotation(
+    gene_data_path, initTable_path=None, df_gene_csv_path=None, df_exon_csv_path=None
+):
     """
     add_gene_annotation
-    for the first 22 chromosomes, retrieves the label of the genes 
+    for the first 22 chromosomes, retrieves the label of the genes
     and their position as well as those of the exons associated with the genes.
     Then store this information in a hdf5 file
-    
+
     :param gene_data_path: path to the GFF file containing gene and exon data (for example, GRCh37_latest_genomic.gff)
     :type gene_data_path: str
     :param initTable_path: path to the file initTable.hdf5
@@ -344,7 +364,7 @@ def add_gene_annotation(gene_data_path,
     :type df_gene_csv_path: str
     :param df_exon_csv_path: path to the file df_exon.csv
     :type df_exon_csv_path: str
-    
+
     :return: the dataframes df_gene and df_exon
     :rtype: 2 PANDAS dataframes
     """
@@ -355,7 +375,7 @@ def add_gene_annotation(gene_data_path,
     gene_start = []
     gene_end = []
     gene_direction = []
-    
+
     # lists containing exon data
     exon_id_label = []
     exon_GeneID = []
@@ -363,7 +383,7 @@ def add_gene_annotation(gene_data_path,
     exon_start = []
     exon_end = []
     exon_direction = []
-    
+
     # temporary list containing the data of all exons
     TMP__exon_id_label = []
     TMP__exon_GeneID = []
@@ -371,18 +391,18 @@ def add_gene_annotation(gene_data_path,
     TMP__exon_start = []
     TMP__exon_end = []
     TMP__exon_direction = []
-    
+
     fichier = open(gene_data_path, "r")
     lignes = fichier.readlines()
     fichier.close()
-    
+
     for ligne in lignes:
         elements = ligne.split("\t")
-        if elements[0].startswith('NC_'):
+        if elements[0].startswith("NC_"):
             decode_chr = elements[0].strip("NC_").split(".")
             chr = int(decode_chr[0])
-            if (chr <= 22):
-                if (elements[2] == "gene"):
+            if chr <= 22:
+                if elements[2] == "gene":
                     gene_chr.append(chr)
                     gene_start.append(int(elements[3]))
                     gene_end.append(int(elements[4]))
@@ -394,8 +414,8 @@ def add_gene_annotation(gene_data_path,
                     decode_id_4 = decode_id_3[0].split("=")
                     decode_id_5 = decode_id_4[1].split(":")
                     gene_GeneID.append(decode_id_5[1])
-                    
-                elif (elements[2] == "exon"):
+
+                elif elements[2] == "exon":
                     TMP__exon_chr.append(chr)
                     TMP__exon_start.append(int(elements[3]))
                     TMP__exon_end.append(int(elements[4]))
@@ -407,49 +427,56 @@ def add_gene_annotation(gene_data_path,
                     decode_id_4 = decode_id_3[0].split("=")
                     decode_id_5 = decode_id_4[1].split(":")
                     TMP__exon_GeneID.append(decode_id_5[1])
-    
-    
-    # We only keep the exons that correspond to a gene 
+
+    # We only keep the exons that correspond to a gene
     for i in range(len(TMP__exon_id_label)):
-        if (TMP__exon_GeneID[i] in gene_GeneID) :
+        if TMP__exon_GeneID[i] in gene_GeneID:
             exon_id_label.append(TMP__exon_id_label[i])
             exon_GeneID.append(TMP__exon_GeneID[i])
             exon_chr.append(TMP__exon_chr[i])
             exon_start.append(TMP__exon_start[i])
             exon_end.append(TMP__exon_end[i])
             exon_direction.append(TMP__exon_direction[i])
-    
+
     # We insert genes and exons into dataframes
-    df_gene = DataFrame({"Chr": gene_chr, 
-                         "GeneID" : gene_GeneID, 
-                         "gene_label" : gene_id_label, 
-                         "start" : gene_start, 
-                         "end" : gene_end, 
-                         "direction" : gene_direction})
-    df_exon = DataFrame({"Chr": exon_chr, 
-                         "exon_label" : exon_id_label, 
-                         "GeneID" : exon_GeneID, 
-                         "start" : exon_start, 
-                         "end" : exon_end, 
-                         "direction" : exon_direction})
-    
+    df_gene = DataFrame(
+        {
+            "Chr": gene_chr,
+            "GeneID": gene_GeneID,
+            "gene_label": gene_id_label,
+            "start": gene_start,
+            "end": gene_end,
+            "direction": gene_direction,
+        }
+    )
+    df_exon = DataFrame(
+        {
+            "Chr": exon_chr,
+            "exon_label": exon_id_label,
+            "GeneID": exon_GeneID,
+            "start": exon_start,
+            "end": exon_end,
+            "direction": exon_direction,
+        }
+    )
+
     # The rows of the dataframes are sorted by chromosome number and start position (and end position for exon)
     df_gene.sort_values(by=["Chr", "start"], inplace=True, ignore_index=True)
     df_exon.sort_values(by=["Chr", "start", "end"], inplace=True, ignore_index=True)
-    
+
     # This information about genes and exons is stored in an hdf5 file if possible
-    if (initTable_path is not None):
+    if initTable_path is not None:
         hdf_file = HDFStore(initTable_path)
         hdf_file.put("Gene", df_gene, format="table", data_columns=True)
         hdf_file.put("Exon", df_exon, format="table", data_columns=True)
         hdf_file.close()
-    
+
     # Dataframe df_gene is stored in a csv file if possible
-    if (df_gene_csv_path is not None):
+    if df_gene_csv_path is not None:
         df_gene.to_csv(df_gene_csv_path)
-    
+
     # Dataframe df_exon is stored in a csv file if possible
-    if (df_exon_csv_path is not None):
+    if df_exon_csv_path is not None:
         df_exon.to_csv(df_exon_csv_path)
-    
-    return (df_gene, df_exon)
\ No newline at end of file
+
+    return (df_gene, df_exon)
diff --git a/jass/models/project.py b/jass/models/project.py
index 7c69033..15a1eb5 100644
--- a/jass/models/project.py
+++ b/jass/models/project.py
@@ -213,16 +213,13 @@ class Project(Model):
         return id_project
 
     def get_global_manhattan_plot_path(self):
-        return os.path.join(self.get_folder_path(), 
-                            "Manhattan_Plot_Omnibus.png")
+        return os.path.join(self.get_folder_path(), "Manhattan_Plot_Omnibus.png")
 
     def get_quadrant_plot_path(self):
-        return os.path.join(self.get_folder_path(), 
-                            "Quadrant_Plot_Omnibus.png")
+        return os.path.join(self.get_folder_path(), "Quadrant_Plot_Omnibus.png")
 
     def get_zoom_plot_path(self):
-        return os.path.join(self.get_folder_path(), 
-                            "Zoom_Plot_Omnibus.png")
+        return os.path.join(self.get_folder_path(), "Zoom_Plot_Omnibus.png")
 
     @property
     def status(self):
diff --git a/jass/models/stats.py b/jass/models/stats.py
index ff2649b..8d6b815 100644
--- a/jass/models/stats.py
+++ b/jass/models/stats.py
@@ -16,21 +16,22 @@ def make_stat_computer_nopattern(cov, stat_func, **kwargs):
     :rtype: function
     """
     # invcov is only computed once
-    invcov = np.linalg.pinv(cov, rcond=0.001)#np.linalg.inv(cov)
+    invcov = np.linalg.pinv(cov, rcond=0.001)  # np.linalg.inv(cov)
 
     def compute(z):
-        return stat_func(z, cov, invcov,**kwargs)
+        return stat_func(z, cov, invcov, **kwargs)
+
     return compute
 
 
 def make_stat_computer_pattern(cov, stat_func):
     """
     Create the function that computes the joint statistics if NaN values are in z
-    and if the number of selected phenotypes is less than or equal to 16. 
+    and if the number of selected phenotypes is less than or equal to 16.
     It uses a covariance matrix corresponding
     to the pattern of non-NaN values in z.
-    This function is implemented using the currying technique: 
-    the first part which declares the data structure and the stat function 
+    This function is implemented using the currying technique:
+    the first part which declares the data structure and the stat function
     is called only once while the second part (compute) is called for each pattern.
     :param cov: covariance matrix
     :type cov: pandas.core.frame.DataFrame
@@ -41,13 +42,15 @@ def make_stat_computer_pattern(cov, stat_func):
     """
     if not stat_func.can_use_pattern:
         raise ValueError("this computation strategy cannot be used with patterns")
-    
+
     # invcov_bypattern is a dictionary of invcovs where the key is the
     # corresponding pattern of non-NaN values in z
     invcov_bypattern = {}
 
     def compute(z, pattern_code):
-        z_na_bool = z.iloc[0,].notnull()
+        z_na_bool = z.iloc[
+            0,
+        ].notnull()
         if pattern_code in invcov_bypattern:
             invcov = invcov_bypattern[pattern_code]
         else:
@@ -67,8 +70,8 @@ def make_stat_computer_pattern_big(cov, stat_func):
     and if the number of selected phenotypes is greater than or equal to 17.
     It uses a covariance matrix corresponding
     to the pattern of non-NaN values in z.
-    This function is implemented using the currying technique: 
-    the first part which declares the data structure and the stat function 
+    This function is implemented using the currying technique:
+    the first part which declares the data structure and the stat function
     is called only once while the second part (compute) is called for each pattern.
     :param cov: covariance matrix
     :type cov: numpy.ndarray
@@ -87,7 +90,7 @@ def make_stat_computer_pattern_big(cov, stat_func):
         if pattern_code in invcov_bypattern:
             invcov = invcov_bypattern[pattern_code]
         else:
-            mini_cov = (cov.take(Num,axis=1)).take(Num,axis=0)
+            mini_cov = (cov.take(Num, axis=1)).take(Num, axis=0)
             invcov = np.linalg.pinv(mini_cov, rcond=0.001)
             invcov_bypattern[pattern_code] = invcov
 
@@ -111,6 +114,7 @@ def make_stat_computer_nan_dumb(cov, stat_func):
 
     return compute
 
+
 def omnibus_stat(z, cov, invcov):
     """
     joint statistics "omnibus" strategy
@@ -163,7 +167,7 @@ def fisher_test(z, cov, invcov):
         print(z)
         print(cov)
         print(invcov)
-        p_val = 2*spst.norm.sf(np.abs(z))
+        p_val = 2 * spst.norm.sf(np.abs(z))
         stat = -2 * np.log(np.nansum(p_val, axis=1))
         return spst.chi2.sf(stat, df=p)
     except ValueError:
@@ -171,8 +175,10 @@ def fisher_test(z, cov, invcov):
         print(invcov.shape)
         print("Error in Fisher stat")
 
+
 fisher_test.can_use_pattern = False
 
+
 def meta_analysis(z, cov, invcov, **kwargs):
     """
     Meta analysis using global sample size to weight z-score
@@ -189,16 +195,16 @@ def meta_analysis(z, cov, invcov, **kwargs):
     :type samp_size : pandas.Series
     """
 
-    Effective_sample_size = kwargs.get('samp_size', None)
+    Effective_sample_size = kwargs.get("samp_size", None)
     if Effective_sample_size is None:
-        raise Error('no sample size available to perform meta_analysis')
+        raise Error("no sample size available to perform meta_analysis")
     else:
-        loading = Effective_sample_size.loc[z.columns]**0.5
+        loading = Effective_sample_size.loc[z.columns] ** 0.5
 
-        M_loadings = np.full(z.shape, loading**2)
+        M_loadings = np.full(z.shape, loading ** 2)
         M_loadings[np.isnan(z)] = 0
 
-        z = np.nan_to_num(z) # fill na with zero
+        z = np.nan_to_num(z)  # fill na with zero
 
         numi = loading.dot(z.transpose())
         deno = np.sqrt(np.sum(M_loadings, axis=1))
@@ -208,8 +214,10 @@ def meta_analysis(z, cov, invcov, **kwargs):
 
         return spst.chi2.sf(stat, df=1)
 
+
 meta_analysis.can_use_pattern = False
 
+
 def sumz_stat(z, cov, invcov, **kwargs):
     """
     joint statistics "sumZ" strategy
@@ -223,7 +231,7 @@ def sumz_stat(z, cov, invcov, **kwargs):
     :return: the joint statistics
     :rtype: numpy.ndarray float64
     """
-    loading = kwargs.get('loadings', None)
+    loading = kwargs.get("loadings", None)
 
     if loading is None:
         p = z.shape[1]
@@ -238,11 +246,11 @@ def sumz_stat(z, cov, invcov, **kwargs):
 
     z = np.nan_to_num(z)
     numi = np.square(loading.dot(z.transpose()))
-    deno = np.einsum('ij,jk,ki->i', M_loadings, cov, M_loadings.T)
+    deno = np.einsum("ij,jk,ki->i", M_loadings, cov, M_loadings.T)
 
     # fill na with 0 = don't take the missing GWAS into account in the test
     stat = numi / deno
     return spst.chi2.sf(stat, df=1)
 
 
-sumz_stat.can_use_pattern = False
\ No newline at end of file
+sumz_stat.can_use_pattern = False
diff --git a/jass/models/worktable.py b/jass/models/worktable.py
index 64042d5..b21ce80 100644
--- a/jass/models/worktable.py
+++ b/jass/models/worktable.py
@@ -61,29 +61,37 @@ def signif(x, digit):
     return round(x, digit - int(math.floor(math.log10(abs(x)))) - 1)
 
 
-def choose_stat_function(smart_na_computation, optim_na, big, function_name, stat_function, sub_cov, **kwargs):
+def choose_stat_function(
+    smart_na_computation, optim_na, big, function_name, stat_function, sub_cov, **kwargs
+):
     if smart_na_computation:
         # If stat is sumz use normal computer even with na
         if function_name == "omnibus_stat":
             if optim_na:
                 if big:
-                    stat_compute = make_stat_computer_pattern_big(sub_cov, stat_function)
+                    stat_compute = make_stat_computer_pattern_big(
+                        sub_cov, stat_function
+                    )
                 else:
                     stat_compute = make_stat_computer_pattern(sub_cov, stat_function)
             else:
                 stat_compute = make_stat_computer_nan_dumb(sub_cov, stat_function)
         else:
             if function_name == "meta_analysis":
-                stat_compute = make_stat_computer_nopattern(sub_cov, stat_function, **kwargs)
+                stat_compute = make_stat_computer_nopattern(
+                    sub_cov, stat_function, **kwargs
+                )
             elif function_name == "sumz_stat":
-                loading_file = kwargs.get('loadings', None)
+                loading_file = kwargs.get("loadings", None)
                 if loading_file is None:
                     # Default loadings would be one for every phenotypes
                     stat_compute = make_stat_computer_nopattern(sub_cov, stat_function)
                 else:
                     loadings = read_csv(loading_file, index_col=0)
                     loadings = loadings.iloc[:, 0]
-                    stat_compute = make_stat_computer_nopattern(sub_cov, stat_function, loadings=loadings)
+                    stat_compute = make_stat_computer_nopattern(
+                        sub_cov, stat_function, loadings=loadings
+                    )
             else:
                 stat_compute = make_stat_computer_nopattern(sub_cov, stat_function)
     else:
@@ -92,39 +100,47 @@ def choose_stat_function(smart_na_computation, optim_na, big, function_name, sta
     return stat_compute
 
 
-def add_signif_status_column(region_sub_tab, significance_treshold=5*10**-8):
+def add_signif_status_column(region_sub_tab, significance_treshold=5 * 10 ** -8):
 
     region_sub_tab["signif_status"] = ""
 
     # blue: significant pvalues for omnibus and univariate tests
-    cond = np.where((region_sub_tab.JASS_PVAL < significance_treshold) & (
-        region_sub_tab.UNIVARIATE_MIN_PVAL < significance_treshold))[0]
+    cond = np.where(
+        (region_sub_tab.JASS_PVAL < significance_treshold)
+        & (region_sub_tab.UNIVARIATE_MIN_PVAL < significance_treshold)
+    )[0]
     region_sub_tab.loc[region_sub_tab.index[cond], "signif_status"] = "Both"
 
     # red: significant pvalues for omnibus test only
-    cond = np.where((region_sub_tab.JASS_PVAL < significance_treshold) & (
-        region_sub_tab.UNIVARIATE_MIN_PVAL > significance_treshold))[0]
+    cond = np.where(
+        (region_sub_tab.JASS_PVAL < significance_treshold)
+        & (region_sub_tab.UNIVARIATE_MIN_PVAL > significance_treshold)
+    )[0]
     region_sub_tab.loc[region_sub_tab.index[cond], "signif_status"] = "Joint"
 
     # green: significant pvalues for univariate test only
-    cond = np.where((region_sub_tab.JASS_PVAL > significance_treshold) & (
-        region_sub_tab.UNIVARIATE_MIN_PVAL < significance_treshold))[0]
-    region_sub_tab.loc[region_sub_tab.index[cond],
-                       "signif_status"] = "Univariate"
+    cond = np.where(
+        (region_sub_tab.JASS_PVAL > significance_treshold)
+        & (region_sub_tab.UNIVARIATE_MIN_PVAL < significance_treshold)
+    )[0]
+    region_sub_tab.loc[region_sub_tab.index[cond], "signif_status"] = "Univariate"
 
     # grey: non significant pvalues
-    cond = np.where((region_sub_tab.JASS_PVAL > significance_treshold) & (
-        region_sub_tab.UNIVARIATE_MIN_PVAL > significance_treshold))[0]
+    cond = np.where(
+        (region_sub_tab.JASS_PVAL > significance_treshold)
+        & (region_sub_tab.UNIVARIATE_MIN_PVAL > significance_treshold)
+    )[0]
     region_sub_tab.loc[region_sub_tab.index[cond], "signif_status"] = "None"
 
     return region_sub_tab
 
 
-def get_region_summary(sum_stat_tab, phenotype_ids, significance_treshold=5*10**-8):
+def get_region_summary(sum_stat_tab, phenotype_ids, significance_treshold=5 * 10 ** -8):
 
     # Select the most significant SNP for the joint test for each region
-    region_sub_tab = sum_stat_tab.sort_values(
-        "JASS_PVAL").groupby("Region").first()  # .reset_index()
+    region_sub_tab = (
+        sum_stat_tab.sort_values("JASS_PVAL").groupby("Region").first()
+    )  # .reset_index()
 
     # add minimum univariate p-value
     univar = sum_stat_tab.groupby("Region").min().UNIVARIATE_MIN_PVAL
@@ -132,18 +148,29 @@ def get_region_summary(sum_stat_tab, phenotype_ids, significance_treshold=5*10**
 
     # Tag SNPs depending on which test is significant
     region_sub_tab.reset_index(inplace=True)
-    region_sub_tab = add_signif_status_column(
-        region_sub_tab, significance_treshold)
+    region_sub_tab = add_signif_status_column(region_sub_tab, significance_treshold)
 
     #  reorder columns
-    region_sub_tab = region_sub_tab[['Region', "MiddlePosition", "snp_ids", "CHR", "position",
-                                     "Ref_allele", "Alt_allele", "JASS_PVAL", "UNIVARIATE_MIN_PVAL",
-                                     "signif_status"] + phenotype_ids]
+    region_sub_tab = region_sub_tab[
+        [
+            "Region",
+            "MiddlePosition",
+            "snp_ids",
+            "CHR",
+            "position",
+            "Ref_allele",
+            "Alt_allele",
+            "JASS_PVAL",
+            "UNIVARIATE_MIN_PVAL",
+            "signif_status",
+        ]
+        + phenotype_ids
+    ]
 
     return region_sub_tab
 
 
-def post_computation_filtering(worktable_chunk, significant_treshold=5*10**-8):
+def post_computation_filtering(worktable_chunk, significant_treshold=5 * 10 ** -8):
     """
     Remove SNPs that seems aberrant: SNPs with a very low p-value that are isolated
      in their region
@@ -155,17 +182,20 @@ def post_computation_filtering(worktable_chunk, significant_treshold=5*10**-8):
     """
 
     def count_nearly_significant(rsnp):
-        return((rsnp.JASS_PVAL < (significant_treshold*20)).sum())
+        return (rsnp.JASS_PVAL < (significant_treshold * 20)).sum()
 
     res = worktable_chunk.groupby("Region").apply(count_nearly_significant)
 
     # select region with only one SNP that is significant which is
-    # suspect
+    # suspect
     reg = res.loc[res == 1].index
 
     for reg_aberant in reg:
-        aberant_SNP = worktable_chunk.loc[worktable_chunk.Region == reg_aberant].sort_values(
-            "JASS_PVAL").index[0]
+        aberant_SNP = (
+            worktable_chunk.loc[worktable_chunk.Region == reg_aberant]
+            .sort_values("JASS_PVAL")
+            .index[0]
+        )
         worktable_chunk.drop(aberant_SNP, inplace=True)
 
     return worktable_chunk
@@ -173,11 +203,12 @@ def post_computation_filtering(worktable_chunk, significant_treshold=5*10**-8):
 
 def compute_pleiotropy_index(W, significance_treshold):
 
-    N_significatif = (2.0 * spst.norm.sf(W.fillna(0,
-                                                  inplace=False).abs()) < significance_treshold).sum(1)
+    N_significatif = (
+        2.0 * spst.norm.sf(W.fillna(0, inplace=False).abs()) < significance_treshold
+    ).sum(1)
     N_pheno = (~W.isnull()).sum(1)
     # pleiotropy index is not meaningful for too few phenotype
-    S = N_significatif/N_pheno
+    S = N_significatif / N_pheno
     S.loc[N_pheno < 4] = np.nan
     return S
 
@@ -191,14 +222,14 @@ def create_worktable_file(
     optim_na: bool = True,
     csv_file: str = None,
     chunk_size: int = 50,
-    significance_treshold=5*10**-8,
+    significance_treshold=5 * 10 ** -8,
     post_filtering=True,
     delayed_gen_csv_file=False,
     chromosome: str = None,
     pos_Start: str = None,
     pos_End: str = None,
     **kwargs
-    ):
+):
 
     """
     Create a worktable file from an initial data table by specifying the
@@ -248,49 +279,107 @@ def create_worktable_file(
     K_POS_MAX = 250000000
 
     # Minimum and maximum limit of regions for each chromosome (multiples of 50)
-    Min_pos_chr = [  0, 100, 250, 400, 500, 600, 700, 800,  900, 1000, 1050,
-                   1150, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1650]
-    Max_pos_chr = [150, 300, 400, 550, 650, 750, 850, 950, 1050, 1100, 1200,
-                   1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1700, 1750]
+    Min_pos_chr = [
+        0,
+        100,
+        250,
+        400,
+        500,
+        600,
+        700,
+        800,
+        900,
+        1000,
+        1050,
+        1150,
+        1250,
+        1300,
+        1350,
+        1400,
+        1450,
+        1500,
+        1550,
+        1600,
+        1650,
+        1650,
+    ]
+    Max_pos_chr = [
+        150,
+        300,
+        400,
+        550,
+        650,
+        750,
+        850,
+        950,
+        1050,
+        1100,
+        1200,
+        1300,
+        1350,
+        1400,
+        1450,
+        1500,
+        1550,
+        1600,
+        1650,
+        1700,
+        1700,
+        1750,
+    ]
 
     N_pheno = len(phenotype_ids)
 
     # Controls the number of phenotypes
-    if (N_pheno > 64):
-        print("ERROR: {} phenotypes are selected. \nThe current version of JASS cannot analyze more than 64 phenotypes" \
-             .format(N_pheno))
+    if N_pheno > 64:
+        print(
+            "ERROR: {} phenotypes are selected. \nThe current version of JASS cannot analyze more than 64 phenotypes".format(
+                N_pheno
+            )
+        )
         raise ValueError("Maximum number of phenotypes exceeded")
-    elif (N_pheno >= 20):
-        print("WARNING: {} phenotypes are selected. The computation will be very long!".format(N_pheno))
+    elif N_pheno >= 20:
+        print(
+            "WARNING: {} phenotypes are selected. The computation will be very long!".format(
+                N_pheno
+            )
+        )
 
-    if (chromosome is None):
+    if chromosome is None:
         local_analysis = False
         print("============== Whole genome analysis ===============")
     else:
         local_analysis = True
         print("============== Local analysis ===============")
-        if not(chromosome.isdigit()):
-            print("ERROR: when performing a local analysis, the chromosome number (between 1 and 22) is mandatory")
-            raise ValueError("create_worktable_file: the required argument chromosome is not a number")
+        if not (chromosome.isdigit()):
+            print(
+                "ERROR: when performing a local analysis, the chromosome number (between 1 and 22) is mandatory"
+            )
+            raise ValueError(
+                "create_worktable_file: the required argument chromosome is not a number"
+            )
         else:
             num_Chr = int(chromosome)
 
-        if ((pos_Start is None) and (pos_End is None)):
+        if (pos_Start is None) and (pos_End is None):
             chromosome_full = True
             print("------ Chromosome : {} ------".format(num_Chr))
         else:
             chromosome_full = False
-            if ((pos_Start is None) or (not pos_Start.isdigit())):
+            if (pos_Start is None) or (not pos_Start.isdigit()):
                 pos_Start = 0
-            if ((pos_End is None) or (not pos_End.isdigit())):
+            if (pos_End is None) or (not pos_End.isdigit()):
                 pos_End = K_POS_MAX
-            print("------ Chromosome : {} ({} - {}) ------".format(num_Chr, pos_Start, pos_End))
+            print(
+                "------ Chromosome : {} ({} - {}) ------".format(
+                    num_Chr, pos_Start, pos_End
+                )
+            )
 
     print("Phenotypes = {}".format(phenotype_ids))
 
     # Initialization of Jass_progress
-    progress_path = os.path.join(os.path.dirname(
-        project_hdf_path), "JASS_progress.txt")
+    progress_path = os.path.join(os.path.dirname(project_hdf_path), "JASS_progress.txt")
     JASS_progress = 0
     file_progress = open(progress_path, "w")
     file_progress.write(str(JASS_progress))
@@ -309,7 +398,9 @@ def create_worktable_file(
 
         if delayed_gen_csv_file:
             # setting a lock to generate the csv_file asynchronously
-            the_lock_path = os.path.join(os.path.dirname(project_hdf_path), "the_lock.txt")
+            the_lock_path = os.path.join(
+                os.path.dirname(project_hdf_path), "the_lock.txt"
+            )
             the_lock = "The lock is set on : workTable.csv is not yet available"
             file_lock = open(the_lock_path, "w")
             file_lock.write(the_lock)
@@ -318,59 +409,66 @@ def create_worktable_file(
     # subset of phenotypes that have been selected
     phenolist = read_hdf(init_file_path, "PhenoList")
     phenolist = phenolist.loc[phenotype_ids]
-    hdf_work.put(
-        "PhenoList", phenolist
-    )
+    hdf_work.put("PhenoList", phenolist)
 
     # subset of covariance matrix for the selected phenotypes
     cov = read_hdf(init_file_path, "COV")
     sub_cov = cov.loc[phenotype_ids, phenotype_ids]
     # Covariance matrix
-    hdf_work.put(
-        "COV", sub_cov, format="table", data_columns=True
-    )
+    hdf_work.put("COV", sub_cov, format="table", data_columns=True)
 
-    #If available extract genetic covariance
+    # If available extract genetic covariance
     try:
         gcov = read_hdf(init_file_path, "GEN_COV")
         sub_gcov = gcov.loc[phenotype_ids, phenotype_ids]
         # Covariance matrix
-        hdf_work.put(
-            "GEN_COV", sub_gcov, format="table", data_columns=True
-        )
+        hdf_work.put("GEN_COV", sub_gcov, format="table", data_columns=True)
     except KeyError:
         print("Genetic correlation not available in inittable. ")
 
-
-
     regions = read_hdf(init_file_path, "Regions").index.tolist()
-    sum_stat_tab_min_itemsizes = {"snp_ids": 80, "Region": 10, "CHR": 5, "Ref_allele" : 70, "Alt_allele":70}
+    sum_stat_tab_min_itemsizes = {
+        "snp_ids": 80,
+        "Region": 10,
+        "CHR": 5,
+        "Ref_allele": 70,
+        "Alt_allele": 70,
+    }
     region_sub_table_min_itemsizes = {
-        "Region": 10, "index": 10, "CHR": 5, "snp_ids": 80, "signif_status": 20,"Ref_allele" : 70, "Alt_allele":70}
+        "Region": 10,
+        "index": 10,
+        "CHR": 5,
+        "snp_ids": 80,
+        "signif_status": 20,
+        "Ref_allele": 70,
+        "Alt_allele": 70,
+    }
 
     smart_na_computation = not (remove_nan)
     module_name, function_name = stat.split(":")
     stat_module = importlib.import_module(module_name)
     stat_fn = getattr(stat_module, function_name)
 
-    if (N_pheno < K_NB_PHENOTYPES_BIG):
+    if N_pheno < K_NB_PHENOTYPES_BIG:
         big = False
         sub_cov_matrix = sub_cov
     else:
         big = True
         sub_cov_matrix = sub_cov.to_numpy()
 
-    stat_compute = choose_stat_function(smart_na_computation,
-                                        optim_na,
-                                        big,
-                                        function_name,
-                                        stat_fn,
-                                        sub_cov_matrix,
-                                        samp_size=phenolist['Effective_sample_size'],
-                                        **kwargs)
+    stat_compute = choose_stat_function(
+        smart_na_computation,
+        optim_na,
+        big,
+        function_name,
+        stat_fn,
+        sub_cov_matrix,
+        samp_size=phenolist["Effective_sample_size"],
+        **kwargs
+    )
 
     # read data by chunks to optimize memory usage
-    if (not local_analysis):
+    if not local_analysis:
         Nchunk = len(regions) // chunk_size + 1
         start_value = 0
     else:
@@ -379,11 +477,14 @@ def create_worktable_file(
         start_value = Min_pos_chr[num_Chr - 1] // chunk_size
 
         # selection criterion in the case of a partial analysis by chromosome and position
-        if (chromosome_full):
+        if chromosome_full:
             Local_criteria = "(CHR == {})".format(chromosome)
         else:
-            Local_criteria = "(CHR == {}) and (position >= {}) and (position <= {})"\
-            .format(chromosome, pos_Start, pos_End)
+            Local_criteria = (
+                "(CHR == {}) and (position >= {}) and (position <= {})".format(
+                    chromosome, pos_Start, pos_End
+                )
+            )
 
     Nsnp_total = 0
     Nsnp_jassed = 0
@@ -394,52 +495,63 @@ def create_worktable_file(
         JASS_progress = round((chunk + 1) * 100 / (Nchunk + 2))
 
         binf = chunk * chunk_size
-        bsup = (chunk+1) * chunk_size
-
-        sum_stat_tab = read_hdf(init_file_path, 'SumStatTab', columns=[
-            'Region', 'CHR', 'position', 'snp_ids', 'Ref_allele', 'Alt_allele', 'MiddlePosition'] + phenotype_ids,
-            where='Region >= {0} and Region < {1}'.format(binf, bsup))
+        bsup = (chunk + 1) * chunk_size
+
+        sum_stat_tab = read_hdf(
+            init_file_path,
+            "SumStatTab",
+            columns=[
+                "Region",
+                "CHR",
+                "position",
+                "snp_ids",
+                "Ref_allele",
+                "Alt_allele",
+                "MiddlePosition",
+            ]
+            + phenotype_ids,
+            where="Region >= {0} and Region < {1}".format(binf, bsup),
+        )
 
         print("Regions {0} to {1}\r".format(binf, bsup))
 
-        if(local_analysis):
+        if local_analysis:
             # Data extraction in the case of a partial analysis
             sum_stat_tab.query(Local_criteria, inplace=True)
 
         # Remake row index unique: IMPORTANT for assignation with .loc
-        sum_stat_tab.dropna(
-            axis=0, subset=phenotype_ids, how=how_dropna, inplace=True
-        )
+        sum_stat_tab.dropna(axis=0, subset=phenotype_ids, how=how_dropna, inplace=True)
         sum_stat_tab.reset_index(drop=True, inplace=True)
 
         if sum_stat_tab.shape[0] == 0:
-            print(
-                "No data available for region {0} to region {1}".format(binf, bsup))
+            print("No data available for region {0} to region {1}".format(binf, bsup))
             continue  # skip region if no data are available
 
         Nsnp_total = Nsnp_total + sum_stat_tab.shape[0]
 
         if remove_nan or stat.split(":")[-1] != "omnibus_stat":
-            sum_stat_tab['JASS_PVAL'] = stat_compute(
-                sum_stat_tab[phenotype_ids])
+            sum_stat_tab["JASS_PVAL"] = stat_compute(sum_stat_tab[phenotype_ids])
         else:
             if not big:
                 # Algorithm optimized for a small number of phenotypes
 
                 # Sort SumStatTab by missing patterns
                 patterns_missing, frequent_pattern = compute_frequent_missing_pattern(
-                    sum_stat_tab[phenotype_ids])
+                    sum_stat_tab[phenotype_ids]
+                )
 
                 sum_stat_tab["patterns_missing"] = patterns_missing
                 z1 = sum_stat_tab[phenotype_ids]
 
                 # Apply the statistic computation by missing patterns
                 for pattern in frequent_pattern:
-                    bool_serie = (patterns_missing == pattern)
+                    bool_serie = patterns_missing == pattern
                     Selection_criteria = sum_stat_tab["patterns_missing"] == pattern
 
                     try:
-                        sum_stat_tab.loc[bool_serie, "JASS_PVAL"] = stat_compute(z1[Selection_criteria], pattern)
+                        sum_stat_tab.loc[bool_serie, "JASS_PVAL"] = stat_compute(
+                            z1[Selection_criteria], pattern
+                        )
                     except ValueError:
                         print("worktable")
 
@@ -447,8 +559,11 @@ def create_worktable_file(
                 # Algorithm optimized for a high number of phenotypes
 
                 # Sort SumStatTab by missing patterns
-                patterns_missing, frequent_pattern, dico_index_y  = \
-                    compute_frequent_missing_pattern_Big(sum_stat_tab[phenotype_ids])
+                (
+                    patterns_missing,
+                    frequent_pattern,
+                    dico_index_y,
+                ) = compute_frequent_missing_pattern_Big(sum_stat_tab[phenotype_ids])
 
                 sum_stat_tab["index"] = sum_stat_tab.index.tolist()
                 sum_stat_tab["patterns_missing"] = patterns_missing
@@ -463,7 +578,9 @@ def create_worktable_file(
                 dico_z = {}
                 dico_index_x = {}
 
-                sum_stat_tab[Liste_colonnes].apply(lambda x: store_pattern(dico_z, dico_index_x, *x), axis=1)
+                sum_stat_tab[Liste_colonnes].apply(
+                    lambda x: store_pattern(dico_z, dico_index_x, *x), axis=1
+                )
 
                 Retour_omnibus_bypattern = {}
 
@@ -471,9 +588,7 @@ def create_worktable_file(
                 for pattern in frequent_pattern:
                     try:
                         Retour_omnibus_bypattern[pattern] = stat_compute(
-                            np.array(dico_z[pattern]),
-                            pattern,
-                            dico_index_y[pattern]
+                            np.array(dico_z[pattern]), pattern, dico_index_y[pattern]
                         )
                     except ValueError:
                         print("worktable")
@@ -482,7 +597,9 @@ def create_worktable_file(
 
                 for pattern in frequent_pattern:
                     for ligne, indice in enumerate(dico_index_x[pattern]):
-                        Retour_omnibus[int(indice)] = (Retour_omnibus_bypattern[pattern])[int(ligne)]
+                        Retour_omnibus[int(indice)] = (
+                            Retour_omnibus_bypattern[pattern]
+                        )[int(ligne)]
 
                 sum_stat_tab["JASS_PVAL"] = Retour_omnibus
 
@@ -490,25 +607,39 @@ def create_worktable_file(
         sum_stat_tab.sort_values(by=["Region", "CHR"], inplace=True)
 
         sum_stat_tab["UNIVARIATE_MIN_PVAL"] = DataFrame(
-            2.0 *
-            spst.norm.sf(sum_stat_tab[phenotype_ids].fillna(
-                0, inplace=False).abs()),
+            2.0
+            * spst.norm.sf(sum_stat_tab[phenotype_ids].fillna(0, inplace=False).abs()),
             index=sum_stat_tab.index,
         ).min(axis=1)
 
-        sum_stat_tab["UNIVARIATE_MIN_QVAL"] = sum_stat_tab["UNIVARIATE_MIN_PVAL"] * \
-            (1-np.isnan(sum_stat_tab[phenotype_ids]).astype(int)).sum(1)
-        sum_stat_tab.loc[sum_stat_tab.UNIVARIATE_MIN_QVAL >
-                         1, "UNIVARIATE_MIN_QVAL"] = 1
+        sum_stat_tab["UNIVARIATE_MIN_QVAL"] = sum_stat_tab["UNIVARIATE_MIN_PVAL"] * (
+            1 - np.isnan(sum_stat_tab[phenotype_ids]).astype(int)
+        ).sum(1)
+        sum_stat_tab.loc[
+            sum_stat_tab.UNIVARIATE_MIN_QVAL > 1, "UNIVARIATE_MIN_QVAL"
+        ] = 1
 
         # Computing pleiotropy
         sum_stat_tab["PLEIOTROPY_INDEX"] = compute_pleiotropy_index(
-            sum_stat_tab[phenotype_ids], significance_treshold)
+            sum_stat_tab[phenotype_ids], significance_treshold
+        )
 
         sum_stat_tab = sum_stat_tab[
-            ["Region", "CHR", "snp_ids", "position", 'Ref_allele', 'Alt_allele',  "MiddlePosition",
-                "JASS_PVAL", "UNIVARIATE_MIN_PVAL", "UNIVARIATE_MIN_QVAL", "PLEIOTROPY_INDEX"]
-            + phenotype_ids]
+            [
+                "Region",
+                "CHR",
+                "snp_ids",
+                "position",
+                "Ref_allele",
+                "Alt_allele",
+                "MiddlePosition",
+                "JASS_PVAL",
+                "UNIVARIATE_MIN_PVAL",
+                "UNIVARIATE_MIN_QVAL",
+                "PLEIOTROPY_INDEX",
+            ]
+            + phenotype_ids
+        ]
 
         if post_filtering:
             sum_stat_tab = post_computation_filtering(sum_stat_tab)
@@ -517,16 +648,16 @@ def create_worktable_file(
             "SumStatTab", sum_stat_tab, min_itemsize=sum_stat_tab_min_itemsizes
         )
 
-        if ((csv_file is not None) and (not delayed_gen_csv_file)):
-            with open(csv_file, 'a') as f:
-                sum_stat_tab.to_csv(f, header=f.tell()==0)
+        if (csv_file is not None) and (not delayed_gen_csv_file):
+            with open(csv_file, "a") as f:
+                sum_stat_tab.to_csv(f, header=f.tell() == 0)
 
         region_sub_table = get_region_summary(
-            sum_stat_tab, phenotype_ids, significance_treshold=significance_treshold)
+            sum_stat_tab, phenotype_ids, significance_treshold=significance_treshold
+        )
 
         hdf_work.append(
-            "Regions",
-            region_sub_table, min_itemsize=region_sub_table_min_itemsizes
+            "Regions", region_sub_table, min_itemsize=region_sub_table_min_itemsizes
         )
 
         file_progress = open(progress_path, "w")
@@ -545,16 +676,24 @@ def create_worktable_file(
         np.array(
             [
                 [
-                    sum((jost_min < significance_treshold) &
-                        (pval_min < significance_treshold)),
-                    sum((jost_min < significance_treshold) &
-                        (pval_min > significance_treshold)),
+                    sum(
+                        (jost_min < significance_treshold)
+                        & (pval_min < significance_treshold)
+                    ),
+                    sum(
+                        (jost_min < significance_treshold)
+                        & (pval_min > significance_treshold)
+                    ),
                 ],
                 [
-                    sum((jost_min > significance_treshold) &
-                        (pval_min < significance_treshold)),
-                    sum((jost_min > significance_treshold) &
-                        (pval_min > significance_treshold)),
+                    sum(
+                        (jost_min > significance_treshold)
+                        & (pval_min < significance_treshold)
+                    ),
+                    sum(
+                        (jost_min > significance_treshold)
+                        & (pval_min > significance_treshold)
+                    ),
                 ],
             ]
         )
@@ -593,10 +732,10 @@ def binary_code_Big(dico_index_y, *args):
 
     Codage = int(Chaine, 2)
 
-    if (not (Codage in dico_index_y)):
+    if not (Codage in dico_index_y):
         dico_index_y[Codage] = []
         for indice, valeur in enumerate(args):
-            if (valeur == 1):
+            if valeur == 1:
                 dico_index_y[Codage].append(indice)
 
     return Codage
@@ -610,7 +749,7 @@ def store_pattern(dico_z, dico_index_x, *colonne):
     Index = int(colonne[0])
     Codage = int(colonne[1])
 
-    if (not (Codage in dico_z)):
+    if not (Codage in dico_z):
         dico_z[Codage] = []
         dico_index_x[Codage] = []
 
@@ -628,10 +767,12 @@ def compute_frequent_missing_pattern(sum_stat_tab):
     """
     Compute the frequency of missing pattern in the dataset
     """
-    Pheno_is_present = 1- sum_stat_tab.isnull()
+    Pheno_is_present = 1 - sum_stat_tab.isnull()
 
     # The coding of patterns missing is not guaranteed if there are more than 64 phenotypes
-    patterns_missing = Pheno_is_present[Pheno_is_present.columns].apply(lambda x: binary_code(*x), axis=1)
+    patterns_missing = Pheno_is_present[Pheno_is_present.columns].apply(
+        lambda x: binary_code(*x), axis=1
+    )
 
     pattern_frequency = patterns_missing.value_counts() / len(patterns_missing)
     n_pattern = pattern_frequency.shape[0]
@@ -647,17 +788,17 @@ def compute_frequent_missing_pattern_Big(sum_stat_tab):
     """
     dico_index_y = {}
 
-    Pheno_is_present = 1- sum_stat_tab.isnull()
+    Pheno_is_present = 1 - sum_stat_tab.isnull()
 
     # The coding of patterns missing is not guaranteed if there are more than 64 phenotypes
-    patterns_missing = Pheno_is_present[Pheno_is_present.columns] \
-                                       .apply(lambda x: binary_code_Big(dico_index_y, *x), axis=1)
-
+    patterns_missing = Pheno_is_present[Pheno_is_present.columns].apply(
+        lambda x: binary_code_Big(dico_index_y, *x), axis=1
+    )
 
     pattern_frequency = patterns_missing.value_counts() / len(patterns_missing)
     n_pattern = pattern_frequency.shape[0]
     print("Number of pattern {}".format(n_pattern))
-    frequent_pattern  = pattern_frequency.index.tolist()
+    frequent_pattern = pattern_frequency.index.tolist()
 
     return patterns_missing, frequent_pattern, dico_index_y
 
@@ -675,11 +816,9 @@ def stringize_dataframe_region_chr(dataframe: DataFrame):
     :return: The dataframe with converted Region and CHR columns
     :rtype: pandas.DataFrame
     """
-    dataframe["Region"] = dataframe["Region"].apply(
-        lambda x: "Region" + str(x))
+    dataframe["Region"] = dataframe["Region"].apply(lambda x: "Region" + str(x))
     dataframe["CHR"] = dataframe["CHR"].apply(lambda x: "chr" + str(x))
-    dataframe["JASS_PVAL"] = dataframe["JASS_PVAL"].apply(
-        lambda x: str(signif(x, 4)))
+    dataframe["JASS_PVAL"] = dataframe["JASS_PVAL"].apply(lambda x: str(signif(x, 4)))
 
     return dataframe
 
@@ -713,19 +852,22 @@ def get_worktable_genomedata(project_hdf_path: str):
     :rtype: str
     """
     region_subtable = stringize_dataframe_region_chr(
-        read_hdf(project_hdf_path, "Regions"))
+        read_hdf(project_hdf_path, "Regions")
+    )
 
-    region_subtable.rename(index=str, columns={
-                           'JASS_PVAL': 'JOSTmin'}, inplace=True)
+    region_subtable.rename(index=str, columns={"JASS_PVAL": "JOSTmin"}, inplace=True)
 
-    region_subtable['PVALmin'] = region_subtable['UNIVARIATE_MIN_PVAL']
-    region_subtable['PVALmin'] = region_subtable['PVALmin']. apply(
-        lambda x: str(signif(x, 4)))
+    region_subtable["PVALmin"] = region_subtable["UNIVARIATE_MIN_PVAL"]
+    region_subtable["PVALmin"] = region_subtable["PVALmin"].apply(
+        lambda x: str(signif(x, 4))
+    )
 
     return region_subtable.to_csv(index=False)
 
 
-def get_worktable_local_manhattan_data(project_hdf_path: str, chromosome: str = None, region: str = None):
+def get_worktable_local_manhattan_data(
+    project_hdf_path: str, chromosome: str = None, region: str = None
+):
     """
     Read and return the SumStatTab dataframe from a worktable file
     for a given chromosome and region for the Manhattan plot
@@ -739,20 +881,24 @@ def get_worktable_local_manhattan_data(project_hdf_path: str, chromosome: str =
     :return: The dataframe subset corresponding to the chromosome and region, as a CSV formatted text
     :rtype: str
     """
-    if ((chromosome is None) and (region is None)):
+    if (chromosome is None) and (region is None):
         # Local analysis : the file project_hdf_path contains only useful information.
         # No data filter is needed
-        dataframe = read_hdf(project_hdf_path, "SumStatTab",
-                             columns=["Region", "CHR", "position",
-                                      "snp_ids", "JASS_PVAL"])
+        dataframe = read_hdf(
+            project_hdf_path,
+            "SumStatTab",
+            columns=["Region", "CHR", "position", "snp_ids", "JASS_PVAL"],
+        )
     else:
         # Genome full analysis
         region_int = region[6:]
         chromosome_int = chromosome[3:]
-        dataframe = read_hdf(project_hdf_path, "SumStatTab",
-                             columns=["Region", "CHR", "position",
-                                      "snp_ids", "JASS_PVAL"],
-                             where=['Region='+str(region_int), 'CHR='+str(chromosome_int)])
+        dataframe = read_hdf(
+            project_hdf_path,
+            "SumStatTab",
+            columns=["Region", "CHR", "position", "snp_ids", "JASS_PVAL"],
+            where=["Region=" + str(region_int), "CHR=" + str(chromosome_int)],
+        )
 
     dataframe = stringize_dataframe_region_chr(dataframe)
     dataframe = dataframe.sort_values("position")
@@ -760,7 +906,9 @@ def get_worktable_local_manhattan_data(project_hdf_path: str, chromosome: str =
     return dataframe.to_csv(index=False)
 
 
-def get_worktable_local_heatmap_data(project_hdf_path: str, chromosome: str = None, region: str = None):
+def get_worktable_local_heatmap_data(
+    project_hdf_path: str, chromosome: str = None, region: str = None
+):
     """
     Read and return the SumStatTab dataframe from a worktable file
     for a given chromosome and region for the Heatmap plot
@@ -775,7 +923,7 @@ def get_worktable_local_heatmap_data(project_hdf_path: str, chromosome: str = No
              pivoted and as a CSV formatted text
     :rtype: str
     """
-    if ((chromosome is None) and (region is None)):
+    if (chromosome is None) and (region is None):
         # Local analysis : the file project_hdf_path contains only useful information.
         # No data filter is needed
         dataframe = read_hdf(project_hdf_path, "SumStatTab")
@@ -783,16 +931,28 @@ def get_worktable_local_heatmap_data(project_hdf_path: str, chromosome: str = No
         # Genome full analysis
         region_int = region[6:]
         chromosome_int = chromosome[3:]
-        dataframe = read_hdf(project_hdf_path, "SumStatTab",
-                             where=['Region='+str(region_int), 'CHR='+str(chromosome_int)])
+        dataframe = read_hdf(
+            project_hdf_path,
+            "SumStatTab",
+            where=["Region=" + str(region_int), "CHR=" + str(chromosome_int)],
+        )
 
     dataframe = stringize_dataframe_region_chr(dataframe)
     dataframe = dataframe.sort_values("position")
-    dataframe.drop(["Region", "CHR", "position", "JASS_PVAL", "MiddlePosition", "UNIVARIATE_MIN_PVAL",
-                    "UNIVARIATE_MIN_QVAL", "PLEIOTROPY_INDEX"],
-                   axis=1,
-                   inplace=True,
-                   )
+    dataframe.drop(
+        [
+            "Region",
+            "CHR",
+            "position",
+            "JASS_PVAL",
+            "MiddlePosition",
+            "UNIVARIATE_MIN_PVAL",
+            "UNIVARIATE_MIN_QVAL",
+            "PLEIOTROPY_INDEX",
+        ],
+        axis=1,
+        inplace=True,
+    )
     dataframe.rename(columns={"snp_ids": "ID"}, inplace=True)
     column_order = list(dataframe.ID)
     pivoted_dataframe = dataframe.pivot_table(columns="ID")
@@ -822,11 +982,10 @@ def create_genome_full_csv(project_hdf_path, csv_file, chunk_size=50, Nchunk=35)
     """
 
     # path of the lock that indicates that the csv file is not available
-    the_lock_path = os.path.join(os.path.dirname(project_hdf_path),
-                                                 "the_lock.txt")
-    if (os.path.isfile(the_lock_path)):
+    the_lock_path = os.path.join(os.path.dirname(project_hdf_path), "the_lock.txt")
+    if os.path.isfile(the_lock_path):
         # The lock is set on
-        if (os.path.isfile(csv_file)):
+        if os.path.isfile(csv_file):
             # An error occurred: the csv file must not exist if the lock is set
             # The existing csv file is deleted
             os.remove(csv_file)
@@ -837,17 +996,20 @@ def create_genome_full_csv(project_hdf_path, csv_file, chunk_size=50, Nchunk=35)
             bsup = (chunk + 1) * chunk_size
 
             # read workTable.hdf5
-            df_for_csv = read_hdf(project_hdf_path, "SumStatTab",
-                where='Region >= {0} and Region < {1}'.format(binf, bsup))
+            df_for_csv = read_hdf(
+                project_hdf_path,
+                "SumStatTab",
+                where="Region >= {0} and Region < {1}".format(binf, bsup),
+            )
 
             # append the data to the csv file
-            with open(csv_file, 'a') as f:
+            with open(csv_file, "a") as f:
                 df_for_csv.to_csv(f, header=f.tell() == 0)
 
         # The lock is deleted
         os.remove(the_lock_path)
 
-    if (os.path.isfile(csv_file)):
+    if os.path.isfile(csv_file):
         The_file_is_available = True
     else:
         The_file_is_available = False
diff --git a/jass/server.py b/jass/server.py
index 68ab121..9945f24 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -336,7 +336,6 @@ class ProjectZoomHeatmapMethodView(MethodView):
                 abort(500)
 
 
-
 @blp_projects.route("/<project_id>/zoomplot")
 class ProjectZoomPlotMethodView(MethodView):
     def get(self, project_id):
diff --git a/jass/tasks.py b/jass/tasks.py
index dede914..a17a8bc 100644
--- a/jass/tasks.py
+++ b/jass/tasks.py
@@ -9,24 +9,25 @@ from flask import Flask
 import jass.models.project
 from jass.models.project import Project, get_file_building_tb_path
 
-from jass.models.plots import (create_global_plot,
-                               create_local_plot,
-                               create_quadrant_plot,
-                               create_qq_plot)
+from jass.models.plots import (
+    create_global_plot,
+    create_local_plot,
+    create_quadrant_plot,
+    create_qq_plot,
+)
+
+from jass.models.worktable import create_worktable_file, create_genome_full_csv
 
-from jass.models.worktable import (create_worktable_file,
-                                   create_genome_full_csv)
-                                  
 from jass.models.phenotype import Phenotype
 from jass.config import config
 
 
 def make_celery(app):
     celery = Celery()
-    if 'CELERY_CONFIG_MODULE' in os.environ:
-        celery.config_from_envvar('CELERY_CONFIG_MODULE')
+    if "CELERY_CONFIG_MODULE" in os.environ:
+        celery.config_from_envvar("CELERY_CONFIG_MODULE")
     else:
-        celery.config_from_object('jass.celeryconfig')
+        celery.config_from_object("jass.celeryconfig")
     celery.conf.update(app.config)
     TaskBase = celery.Task
 
@@ -41,45 +42,46 @@ def make_celery(app):
     return celery
 
 
-
 flask_app = Flask(__name__)
 celery = make_celery(flask_app)
 
+
 @celery.task
 def create_project_worktable_file(
-        phenotype_ids, 
-        init_file_path, 
-        project_hdf_path, 
-        remove_nan,
-        stat,
-        optim_na,
-        csv_file,
-        chunk_size,
-        significance_treshold,
-        post_filtering,
-        delayed_gen_csv_file,
-        chromosome,
-        pos_Start,
-        pos_End,
-        custom_loadings):
+    phenotype_ids,
+    init_file_path,
+    project_hdf_path,
+    remove_nan,
+    stat,
+    optim_na,
+    csv_file,
+    chunk_size,
+    significance_treshold,
+    post_filtering,
+    delayed_gen_csv_file,
+    chromosome,
+    pos_Start,
+    pos_End,
+    custom_loadings,
+):
     try:
         return create_worktable_file(
-                phenotype_ids = phenotype_ids, 
-                init_file_path = init_file_path, 
-                project_hdf_path = project_hdf_path, 
-                remove_nan = remove_nan,
-                stat = stat,
-                optim_na = True,
-                csv_file = csv_file,
-                chunk_size = chunk_size,
-                significance_treshold = significance_treshold,
-                post_filtering = post_filtering,
-                delayed_gen_csv_file = delayed_gen_csv_file,
-                chromosome = chromosome,
-                pos_Start = pos_Start,
-                pos_End = pos_End,
-                custom_loadings = custom_loadings
-                )
+            phenotype_ids=phenotype_ids,
+            init_file_path=init_file_path,
+            project_hdf_path=project_hdf_path,
+            remove_nan=remove_nan,
+            stat=stat,
+            optim_na=True,
+            csv_file=csv_file,
+            chunk_size=chunk_size,
+            significance_treshold=significance_treshold,
+            post_filtering=post_filtering,
+            delayed_gen_csv_file=delayed_gen_csv_file,
+            chromosome=chromosome,
+            pos_Start=pos_Start,
+            pos_End=pos_End,
+            custom_loadings=custom_loadings,
+        )
     except Exception as e:
         exc_type, exc_value, exc_traceback = sys.exc_info()
         log_path = get_file_building_tb_path(project_hdf_path)
@@ -147,77 +149,78 @@ def create_project_csv_file(Nchunk, worktable_path, csv_file_path):
         traceback.print_exception(exc_type, exc_value, exc_traceback, file=log_fh)
         log_fh.close()
 
+
 def launch_create_project(
-    phenotype_ids, 
-    init_table_path, 
+    phenotype_ids,
+    init_table_path,
     worktable_path,
-    remove_nan = False,
-    stat = "jass.models.stats:omnibus_stat",
-    csv_file = None,
-    chunk_size = 50,
-    significance_treshold = 5*10**-8,
-    post_filtering = True,
-    delayed_gen_csv_file = False,
-    chromosome = None,
-    start = None,
-    end = None,
-    custom_loadings = None,
-    global_plot_path = None, 
-    quadrant_plot_path = None,
-    zoom_plot_path = None,
-    qq_plot_path = None
-    ):
+    remove_nan=False,
+    stat="jass.models.stats:omnibus_stat",
+    csv_file=None,
+    chunk_size=50,
+    significance_treshold=5 * 10 ** -8,
+    post_filtering=True,
+    delayed_gen_csv_file=False,
+    chromosome=None,
+    start=None,
+    end=None,
+    custom_loadings=None,
+    global_plot_path=None,
+    quadrant_plot_path=None,
+    zoom_plot_path=None,
+    qq_plot_path=None,
+):
     post_worktable_jobs = []
-    if (global_plot_path is not None):
+    if global_plot_path is not None:
         post_worktable_jobs.append(
             create_project_global_plot.si(worktable_path, global_plot_path)
         )
-    if (quadrant_plot_path is not None):
+    if quadrant_plot_path is not None:
         post_worktable_jobs.append(
             create_project_quadrant_plot.si(worktable_path, quadrant_plot_path),
         )
-    if (zoom_plot_path is not None):
+    if zoom_plot_path is not None:
         post_worktable_jobs.append(
             create_project_zoom_plot.si(worktable_path, zoom_plot_path)
         )
-    if (qq_plot_path is not None):
+    if qq_plot_path is not None:
         post_worktable_jobs.append(
             create_project_qq_plot.si(worktable_path, qq_plot_path)
         )
-    if (delayed_gen_csv_file and (csv_file is not None)):
-        post_worktable_jobs.append(
-            create_project_csv_file.s(worktable_path, csv_file)
-        )
+    if delayed_gen_csv_file and (csv_file is not None):
+        post_worktable_jobs.append(create_project_csv_file.s(worktable_path, csv_file))
     post_worktable_tasks_group = group(post_worktable_jobs)
-    main_wf = chain(create_project_worktable_file.si(
-                phenotype_ids = phenotype_ids, 
-                init_file_path = init_table_path, 
-                project_hdf_path = worktable_path, 
-                remove_nan = remove_nan,
-                stat = stat,
-                optim_na = True,
-                csv_file = csv_file,
-                chunk_size = chunk_size,
-                significance_treshold = significance_treshold,
-                post_filtering = post_filtering,
-                delayed_gen_csv_file = delayed_gen_csv_file,
-                chromosome = chromosome,
-                pos_Start = start,
-                pos_End = end,
-                custom_loadings = custom_loadings
-                ),
-                post_worktable_tasks_group)
+    main_wf = chain(
+        create_project_worktable_file.si(
+            phenotype_ids=phenotype_ids,
+            init_file_path=init_table_path,
+            project_hdf_path=worktable_path,
+            remove_nan=remove_nan,
+            stat=stat,
+            optim_na=True,
+            csv_file=csv_file,
+            chunk_size=chunk_size,
+            significance_treshold=significance_treshold,
+            post_filtering=post_filtering,
+            delayed_gen_csv_file=delayed_gen_csv_file,
+            chromosome=chromosome,
+            pos_Start=start,
+            pos_End=end,
+            custom_loadings=custom_loadings,
+        ),
+        post_worktable_tasks_group,
+    )
     main_wf.delay()
 
 
 def create_project(
-    phenotype_ids: List[str], 
+    phenotype_ids: List[str],
     available_phenotypes: List[Phenotype],
     chromosome: str = None,
     start: str = None,
-    end: str = None
-    ):
-    
+    end: str = None,
+):
+
     available_phenotype_ids = [phenotype.id for phenotype in available_phenotypes]
     unavailable_requested_ids = set(phenotype_ids).difference(
         set(available_phenotype_ids)
@@ -227,12 +230,11 @@ def create_project(
     phenotypes = [
         phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
     ]
-    project = Project(phenotypes = phenotypes, 
-                      chromosome = chromosome, 
-                      start = start, 
-                      end = end)
-    
-    if (project.get_type_of_analysis() == Project.LOCAL_ANALYSIS):
+    project = Project(
+        phenotypes=phenotypes, chromosome=chromosome, start=start, end=end
+    )
+
+    if project.get_type_of_analysis() == Project.LOCAL_ANALYSIS:
         # Local Analysis
         global_plot_path = None
         quadrant_plot_path = None
@@ -244,21 +246,21 @@ def create_project(
         quadrant_plot_path = project.get_quadrant_plot_path()
         zoom_plot_path = None
         delayed_gen_csv_file = True
-    
+
     # if project does not exist
     if project.status == Project.DOES_NOT_EXIST:
         os.makedirs(project.get_folder_path())
         launch_create_project(
-            phenotype_ids = phenotype_ids,
-            init_table_path = os.path.join(config["DATA_DIR"], "initTable.hdf5"),
-            worktable_path = project.get_worktable_path(),
-            csv_file = project.get_csv_path(),
-            global_plot_path = global_plot_path,
-            quadrant_plot_path = quadrant_plot_path,
-            zoom_plot_path = zoom_plot_path,
-            delayed_gen_csv_file = delayed_gen_csv_file,
-            chromosome = chromosome,
-            start = start,
-            end = end
+            phenotype_ids=phenotype_ids,
+            init_table_path=os.path.join(config["DATA_DIR"], "initTable.hdf5"),
+            worktable_path=project.get_worktable_path(),
+            csv_file=project.get_csv_path(),
+            global_plot_path=global_plot_path,
+            quadrant_plot_path=quadrant_plot_path,
+            zoom_plot_path=zoom_plot_path,
+            delayed_gen_csv_file=delayed_gen_csv_file,
+            chromosome=chromosome,
+            start=start,
+            end=end,
         )
-    return project
\ No newline at end of file
+    return project
diff --git a/jass/test/__init__.py b/jass/test/__init__.py
index 7ddc6ba..5dae7a4 100644
--- a/jass/test/__init__.py
+++ b/jass/test/__init__.py
@@ -11,6 +11,7 @@ import flask_testing
 # to avoid freezing calls in unit tests
 from celery.app.task import Task
 from unittest.mock import MagicMock
+
 Task.delay = MagicMock()
 Task.si = MagicMock()
 
@@ -29,6 +30,7 @@ class JassTestCase(unittest.TestCase):
 class JassFlaskTestCase(JassTestCase, flask_testing.TestCase):
     def create_app(self):
         from jass.config import config
+
         self.test_dir = tempfile.mkdtemp()
         config["DATA_DIR"] = self.test_dir
         shutil.copy(self.get_file_path_fn("initTable.hdf5"), self.test_dir)
diff --git a/jass/test/test_init_table.py b/jass/test/test_init_table.py
index 5df8b9a..d0a428f 100644
--- a/jass/test/test_init_table.py
+++ b/jass/test/test_init_table.py
@@ -40,20 +40,24 @@ class TestInitTable(object):
 
     def tearDown(self):
         # Remove the directory after the test
-        #shutil.rmtree(self.test_dir)
+        # shutil.rmtree(self.test_dir)
         print(self.test_dir)
 
     def test_compare_phenolist(self):
         """
         Compare result and expected PhenoList
         """
-        assert_frame_equal(self.expected_phenolist, self.result_phenolist, check_like=True)
+        assert_frame_equal(
+            self.expected_phenolist, self.result_phenolist, check_like=True
+        )
 
     def test_compare_sumstattab(self):
         """
         Compare result and expected SumStatTab
         """
-        assert_frame_equal(self.expected_sum_stat_tab, self.result_sum_stat_tab, check_like=True)
+        assert_frame_equal(
+            self.expected_sum_stat_tab, self.result_sum_stat_tab, check_like=True
+        )
 
     def test_compare_cov(self):
         """
diff --git a/jass/test/test_plots.py b/jass/test/test_plots.py
index 9bdbdf0..7748ccb 100644
--- a/jass/test/test_plots.py
+++ b/jass/test/test_plots.py
@@ -32,6 +32,7 @@ class TestPlots(JassTestCase):
         """
         create_global_plot(self.worktable_hdf_path, self.global_plot_path)
 
+
 if __name__ == "__main__":
     import unittest
 
diff --git a/jass/test/test_server.py b/jass/test/test_server.py
index da1b771..9bf088b 100644
--- a/jass/test/test_server.py
+++ b/jass/test/test_server.py
@@ -11,22 +11,26 @@ from . import JassFlaskTestCase
 
 
 class TestDefaultController(JassFlaskTestCase):
-    """ DefaultController integration test stubs """
+    """DefaultController integration test stubs"""
 
     test_folder = "data_test1"
 
     def test_phenotypes_get(self):
         """
-        Test case retrieving available phenotypes        
+        Test case retrieving available phenotypes
         """
         response = self.testing_client.open("/api/phenotypes/", method="GET")
         self.assert200(response, "Response body is : " + response.data.decode("utf-8"))
 
     def test_create_project(self):
         """
-        Test case for creating a project        
+        Test case for creating a project
         """
-        response = self.testing_client.open("/api/projects/", method="POST",data={"phenotypeID":"z_IHEC_MONOP,z_RA_RA"})
+        response = self.testing_client.open(
+            "/api/projects/",
+            method="POST",
+            data={"phenotypeID": "z_IHEC_MONOP,z_RA_RA"},
+        )
         self.assert200(response, "Response body is : " + response.data.decode("utf-8"))
 
 
diff --git a/jass/test/test_worktable.py b/jass/test/test_worktable.py
index bed2941..5e9b3ce 100644
--- a/jass/test/test_worktable.py
+++ b/jass/test/test_worktable.py
@@ -47,19 +47,25 @@ class TestWorkTable(object):
         """
         Compare result and expected SumStatJostTab
         """
-        assert_frame_equal(self.expected_sumstatjosttab, self.result_sumstatjosttab, check_like=True)
+        assert_frame_equal(
+            self.expected_sumstatjosttab, self.result_sumstatjosttab, check_like=True
+        )
 
     def test_compare_regionsubtable(self):
         """
         Compare result and expected RegionSubTable
         """
-        assert_frame_equal(self.expected_regionsubtable, self.result_regionsubtable, check_like=True)
+        assert_frame_equal(
+            self.expected_regionsubtable, self.result_regionsubtable, check_like=True
+        )
 
     def test_compare_summarytable(self):
         """
         Compare result and expected SummaryTable
         """
-        assert_frame_equal(self.expected_summarytable, self.result_summarytable, check_like=True)
+        assert_frame_equal(
+            self.expected_summarytable, self.result_summarytable, check_like=True
+        )
 
     def test_compare_subcov(self):
         """
@@ -71,8 +77,9 @@ class TestWorkTable(object):
         """
         Compare result and expected PhenoList
         """
-        assert_frame_equal(self.expected_phenolist, self.result_phenolist, check_like=True)
-
+        assert_frame_equal(
+            self.expected_phenolist, self.result_phenolist, check_like=True
+        )
 
 
 phenotypes_disney = ["z_DISNEY_POCAHONT", "z_DISNEY_RATATOUY"]
diff --git a/jass/util.py b/jass/util.py
index 4e0189d..6c0445b 100644
--- a/jass/util.py
+++ b/jass/util.py
@@ -68,6 +68,7 @@ def deserialize_date(string):
     """
     try:
         from dateutil.parser import parse
+
         return parse(string).date()
     except ImportError:
         return string
@@ -85,6 +86,7 @@ def deserialize_datetime(string):
     """
     try:
         from dateutil.parser import parse
+
         return parse(string)
     except ImportError:
         return string
@@ -104,9 +106,11 @@ def deserialize_model(data, klass):
         return data
 
     for attr, attr_type in six.iteritems(instance.swagger_types):
-        if data is not None \
-                and instance.attribute_map[attr] in data \
-                and isinstance(data, (list, dict)):
+        if (
+            data is not None
+            and instance.attribute_map[attr] in data
+            and isinstance(data, (list, dict))
+        ):
             value = data[instance.attribute_map[attr]]
             setattr(instance, attr, _deserialize(value, attr_type))
 
@@ -123,8 +127,7 @@ def _deserialize_list(data, boxed_type):
     :return: deserialized list.
     :rtype: list
     """
-    return [_deserialize(sub_data, boxed_type)
-            for sub_data in data]
+    return [_deserialize(sub_data, boxed_type) for sub_data in data]
 
 
 def _deserialize_dict(data, boxed_type):
@@ -137,5 +140,4 @@ def _deserialize_dict(data, boxed_type):
     :return: deserialized dict.
     :rtype: dict
     """
-    return {k: _deserialize(v, boxed_type)
-            for k, v in six.iteritems(data)}
\ No newline at end of file
+    return {k: _deserialize(v, boxed_type) for k, v in six.iteritems(data)}
-- 
GitLab


From 1990de8351055c10b11394672cf66cf80110fa74 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Thu, 8 Jul 2021 14:38:52 +0200
Subject: [PATCH 19/25] remove unused "controllers" package

---
 jass/controllers/__init__.py | 10 ----------
 1 file changed, 10 deletions(-)
 delete mode 100644 jass/controllers/__init__.py

diff --git a/jass/controllers/__init__.py b/jass/controllers/__init__.py
deleted file mode 100644
index 38c0339..0000000
--- a/jass/controllers/__init__.py
+++ /dev/null
@@ -1,10 +0,0 @@
-"""
-the list of controller functions called by the JASS REST web services
-
-Submodules
-==========
-
-.. autosummary::
-    :toctree: _autosummary
-
-"""
-- 
GitLab


From 618664bf1a0cfdcbdb729e570a7966944e94d90a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Thu, 8 Jul 2021 15:58:58 +0200
Subject: [PATCH 20/25] correct and clean-up swagger file

---
 jass/swagger/swagger.yaml | 1140 ++++++++++++++++++-------------------
 1 file changed, 566 insertions(+), 574 deletions(-)

diff --git a/jass/swagger/swagger.yaml b/jass/swagger/swagger.yaml
index c61ff5b..03378e6 100644
--- a/jass/swagger/swagger.yaml
+++ b/jass/swagger/swagger.yaml
@@ -1,574 +1,566 @@
-openapi: 3.0.0
-info:
-  version: 0.0.0
-  title: JASS API Specification
-paths:
-  /phenotypes:
-    get:
-      description: |
-        Gets the list of available phenotypes
-      operationId: phenotypes_get
-      responses:
-        "200":
-          description: List of the available phenotypes
-          content:
-            "application/json":
-              schema:
-                type: array
-                title: ArrayOfPhenotypes
-                items:
-                  $ref: "#/components/schemas/Phenotype"
-              example:
-                - "consortium": "IHEC"
-                  "data_link": "http://www.bloodcellgenetics.org"
-                  "full_name": "Monocyte percentage of white cells"
-                  "id": "z_IHEC_MONOP"
-                  "outcome": "MONOP"
-                  "ref": " Astle et al. 2016"
-                  "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/27863262"
-                  "type": "Cellular"
-                - "consortium": "RA"
-                  "data_link": "http://plaza.umin.ac.jp/~yokada/datasource/software.htm"
-                  "full_name": "Rheumatoid Arthritis"
-                  "id": "z_RA_RA"
-                  "outcome": "RA"
-                  "ref": "Okada et al. 2014"
-                  "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/24390342"
-                  "type": "Immunity"
-  /projects:
-    post:
-      description: |
-        Create a new project from a selection of phenotypes
-      operationId: projects_post
-      requestBody:
-        content:
-          application/x-www-form-urlencoded:
-            schema:
-              type: object
-              properties:
-                phenotypeID:
-                  description: IDs of the phenotypes selected for the project
-                  type: array
-                  items:
-                    type: string
-              required:
-                - phenotypeID
-            example:
-              - z_IHEC_MONOP
-              - z_RA_RA
-      responses:
-        "200":
-          description: Project created
-          content:
-            "application/json":
-              schema:
-                $ref: "#/components/schemas/Phenotype"
-              examples:
-                Creating:
-                  value:
-                    id: "bca9d414e0f9a67b9e0d2131a47c316c"
-                    phenotypes:
-                      - "consortium": "IHEC"
-                        "data_link": "http://www.bloodcellgenetics.org"
-                        "full_name": "Monocyte percentage of white cells"
-                        "id": "z_IHEC_MONOP"
-                        "outcome": "MONOP"
-                        "ref": " Astle et al. 2016"
-                        "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/27863262"
-                        "type": "Cellular"
-                      - "consortium": "RA"
-                        "data_link": "http://plaza.umin.ac.jp/~yokada/datasource/software.htm"
-                        "full_name": "Rheumatoid Arthritis"
-                        "id": "z_RA_RA"
-                        "outcome": "RA"
-                        "ref": "Okada et al. 2014"
-                        "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/24390342"
-                        "type": "Immunity"
-                    status":
-                        "global_manhattan": "CREATING"
-                        "quadrant_plot_status": "CREATING"
-                        "worktable": "CREATING"
-                    progress":
-                        "progress": "0"
-                Ready:
-                  value:
-                    id: "bca9d414e0f9a67b9e0d2131a47c316c"
-                    phenotypes:
-                      - "consortium": "IHEC"
-                        "data_link": "http://www.bloodcellgenetics.org"
-                        "full_name": "Monocyte percentage of white cells"
-                        "id": "z_IHEC_MONOP"
-                        "outcome": "MONOP"
-                        "ref": " Astle et al. 2016"
-                        "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/27863262"
-                        "type": "Cellular"
-                      - "consortium": "RA"
-                        "data_link": "http://plaza.umin.ac.jp/~yokada/datasource/software.htm"
-                        "full_name": "Rheumatoid Arthritis"
-                        "id": "z_RA_RA"
-                        "outcome": "RA"
-                        "ref": "Okada et al. 2014"
-                        "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/24390342"
-                        "type": "Immunity"
-                    status":
-                        "global_manhattan": "READY"
-                        "quadrant_plot_status": "READY"
-                        "worktable": "READY"
-                    progress":
-                        "progress": "100"
-  "/local_project/{chromosome}/{start}/{end}":
-    post:
-      description: |
-        Create a new local project from a selection of phenotypes
-      operationId: local_project_post
-      parameters:
-      - name: chromosome
-        in: path
-        description: chromosome number
-        required: true
-        schema:
-           type: string
-      - name: start
-        in: path
-        description: start position of the region
-        required: true
-        schema:
-           type: string
-      - name: end
-        in: path
-        description: end position of the region
-        required: true
-        schema:
-           type: string
-      requestBody:
-        content:
-          application/x-www-form-urlencoded:
-            schema:
-              type: object
-              properties:
-                phenotypeID:
-                  description: IDs of the phenotypes selected for the project
-                  type: array
-                  items:
-                    type: string
-              required:
-                - phenotypeID               
-      responses:
-        "200":
-          description: Project created
-          content:
-            "application/json":
-              schema:
-                $ref: "#/components/schemas/Phenotype"
-  "/projects/{projectID}":
-    get:
-      description: |
-        Retrieve a project definition
-      operationId: projects_project_idget
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-      responses:
-        "200":
-          description: Retrieved project
-          content:
-            "application/json":
-              schema:
-                $ref: "#/components/schemas/Phenotype"
-              example:
-                id: "bca9d414e0f9a67b9e0d2131a47c316c"
-                status":
-                    "global_manhattan": "READY"
-                    "quadrant_plot_status": "READY"
-                    "worktable": "READY"
-                progress":
-                    "progress": "100"
-  "/projects/{projectID}/summary":
-    get:
-      description: Retrieve summary statistics for a given project
-      operationId: projects_project_id_summary_statistics
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-      responses:
-        "200":
-          description: Summary statistics in JSON
-          content:
-            "*/*":
-              schema:
-                type: string
-                title: Project summary statistics
-              example:
-                "JOSTSignif":
-                  "NoPhenoSignif": 10
-                  "PhenoSignif": 210
-                "NoJOSTSignif":
-                  "NoPhenoSignif": 1470
-                  "PhenoSignif": 14
-  "/projects/{projectID}/csv_status":
-    get:
-      description: |
-        Retrieve the generation status of the genome full csv file
-      operationId: projects_project_id_csv_status_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-      responses:
-        "200":
-          description: |
-            Generation status of the genome full csv file
-          content:
-            text/csv; charset=utf-8:
-              schema:
-                type: string
-                title: csv_file_generation
-              example: |
-                READY
-  "/projects/{projectID}/genome":
-    get:
-      description: |
-        Retrieve whole genome summary data for a given project
-      operationId: projects_project_id_genome_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-      responses:
-        "200":
-          description: |
-            Whole genome summary data in CSV format
-          content:
-            text/csv; charset=utf-8:
-              schema:
-                type: string
-                title: Genome data
-              example: |
-                Region,MiddlePosition,snp_ids,CHR,position,Ref_allele,Alt_allele,JOSTmin,UNIVARIATE_MIN_PVAL,signif_status,z_IHEC_MONOP,z_RA_RA
-                Region0,0.0,rs61997853,chr15,20001087,C,A,0.3085010612493116,0.300300000000003,None,-1.0357902654077036,
-                Region1,951595.0,rs28635530,chr1,1649392,T,C,4.038788020606384e-06,2.7559999999999873e-06,None,4.688213804974398,2.999976992703393
-                Region2,2737671.5,rs72644697,chr1,2533605,A,G,2.4600636176583336e-10,1.6188949607934016e-10,Both,-1.4356568827860683,-6.393727818324495
-                Region3,3981773.5,rs12145992,chr1,3760309,A,G,0.0002538976722549933,0.00026034845141981964,None,-1.6164363711150218,3.651859369008055
-                Region4,5147352.0,rs2649072,chr1,5754088,G,A,0.0007863952492527496,0.0006378999999999985,None,3.4149658871961184,-2.999976992703393
-                Region5,6580614.0,rs2986741,chr1,6548774,G,A,0.0013472918321710914,0.0011119999999999993,None,-3.260540717377886,2.726551316504396
-                Region6,8306267.0,rs79412885,chr1,9241839,A,G,2.0889091093474285e-13,8.106999999999937e-14,Both,7.46857160133221,-1.2003588580308502
-                Region7,10086091.5,rs113829298,chr1,10061038,T,C,4.3158209846991565e-05,6.135999999999996e-06,None,-4.5216481219798474,0.5100734569685951
-  "/projects/{projectID}/genome_full":
-    get:
-      description: |
-        Retrieve whole genome complete (not summarized) data for a given project
-      operationId: projects_project_id_genome_full_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-      responses:
-        "200":
-          description: >
-            Retrieve whole genome complete (not summarized) data for a given
-            project in CSV format
-          content:
-            text/csv; charset=utf-8:
-              schema:
-                type: string
-                title: Genome data
-              example: |
-                Region,CHR,snp_ids,position,Ref_allele,Alt_allele,MiddlePosition,JASS_PVAL,UNIVARIATE_MIN_PVAL,UNIVARIATE_MIN_QVAL,PLEIOTROPY_INDEX,z_IHEC_MONOP,z_RA_RA
-                194218,0,6,rs530120680,63980,G,A,0.0,0.6556994470547299,0.6501999999999999,0.6501999999999999,,0.4534843639637209,
-                194219,0,6,rs561313667,63979,T,C,0.0,0.538722344719537,0.5318,0.5318,,0.6252606526209208,
-                194220,0,15,rs113772187,20000538,T,C,0.0,0.5218942699938458,0.5148000000000001,0.5148000000000001,,-0.651381887083556,
-                194221,0,15,rs61997852,20001079,C,A,0.0,0.33819737748654505,0.33000000000000274,0.33000000000000274,,-0.9741138770593036,
-                194222,0,15,rs61997853,20001087,C,A,0.0,0.3085010612493116,0.300300000000003,0.300300000000003,,-1.0357902654077036,
-                867,1,1,rs10454464,1833495,A,G,951595.0,0.2523888759643953,0.19000000000000383,0.38000000000000766,,-0.9817967289175548,1.3105791121681174
-                4836,1,1,rs10907175,1130727,C,A,951595.0,0.3313846158840952,0.21180000000000354,0.4236000000000071,,1.2486311872236304,0.8380752842791193
-                4837,1,1,rs10907176,1130855,C,T,951595.0,0.3455642965805482,0.2251000000000033,0.4502000000000066,,1.213078000845954,0.8380752842791193
-                4838,1,1,rs10907185,1733219,A,G,951595.0,0.3919109214945312,0.25000000000000333,0.5000000000000067,,-0.7010048315295425,1.1503493803760003
-                4839,1,1,rs10907187,1759054,A,G,951595.0,0.16161974795348924,0.09099999999999998,0.18199999999999997,,-0.8114627085037827,1.6901461375274702
-                4840,1,1,rs10907188,1768894,T,C,951595.0,0.15366147518120524,0.08599999999999992,0.17199999999999985,,-0.8149516264832889,1.7168860184310413
-                4841,1,1,rs10907190,1773772,A,G,951595.0,0.12979175667585227,0.07999999999999982,0.15999999999999964,,-0.938281041511616,1.7506860712521708
-                4842,1,1,rs10907193,1805391,A,G,951595.0,0.09562672355608258,0.06299999999999988,0.12599999999999975,,-1.0405165049626888,1.8591914944718688
-                4843,1,1,rs10907194,1712230,T,C,951595.0,0.2669995168398967,0.16000000000000425,0.3200000000000085,,-0.7600913211933399,1.4050715603096189
-  "/projects/{projectID}/globalmanhattan":
-    get:
-      description: |
-        Retrieve global manhattan plot for a given project
-      operationId: projects_project_id_global_manhattan_plot_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-      responses:
-        "200":
-          description: |
-            Global manhattan plot in PNG format
-          content:
-            image/png:
-              schema:
-                type: string
-                title: Global manhattan plot
-              example:
-                externalValue: 'globalmanhattan_example.png'
-  "/projects/{projectID}/zoomplot":
-    get:
-      description: |
-        Retrieve zoom plot for a given local project
-      operationId: projects_project_id_zoom_plot_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-      responses:
-        "200":
-          description: |
-            Zoom plot in PNG format
-          content:
-            image/png:
-              schema:
-                type: string
-                title: Zoom plot
-  "/projects/{projectID}/quadrant":
-    get:
-      description: |
-        Retrieve quadrant plot for a given project
-      operationId: projects_project_id_quadrant_plot_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-      responses:
-        "200":
-          description: |
-            Quadrant plot in PNG format
-          content:
-            image/png:
-              schema:
-                type: string
-                title: Quadrant plot
-              example:
-                externalValue: 'quadrant_example.png'
-  "/projects/{projectID}/manhattan/{chromosome}/{region}":
-    get:
-      description: Retrieve local manhattan data
-      operationId: projects_project_id_local_manhattan_data_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-        - name: chromosome
-          in: path
-          description: chromosome number
-          required: true
-          schema:
-            type: string
-          example: "chr1"
-        - name: region
-          in: path
-          description: region number
-          required: true
-          schema:
-            type: string
-          example: "Region1"
-      responses:
-        "200":
-          description: |
-            Local manhattan plot data in CSV format
-          content:
-            text/csv; charset=utf-8:
-              schema:
-                type: string
-                title: Local manhattan plot data
-              example: |
-                Region,CHR,position,snp_ids,JASS_PVAL
-                Region1,chr1,636285,rs545945172,0.7216577092326355
-                Region1,chr1,662414,rs371628865,0.6725666758876788
-                Region1,chr1,662622,rs61769339,0.405683282952658
-                Region1,chr1,665266,rs539032812,0.3348008598497511
-                Region1,chr1,693731,rs12238997,0.4952464035829177
-                Region1,chr1,701835,rs189800799,0.666563580963709
-                Region1,chr1,706778,rs113462541,0.861641963454806
-                Region1,chr1,711310,rs200531508,0.07463266395489108
-                Region1,chr1,714019,rs114983708,0.6667198743938074
-                Region1,chr1,715265,rs12184267,0.6666055494294745
-                Region1,chr1,715367,rs12184277,0.7657858702655146
-                Region1,chr1,720381,rs116801199,0.6816390671665746
-                Region1,chr1,723742,rs28375378,0.7124933618852456
-                Region1,chr1,724324,rs28692873,0.9212425499680825
-                Region1,chr1,725196,rs377099097,0.594983644175122
-                Region1,chr1,725389,rs375619475,0.7032290172253173
-                Region1,chr1,727841,rs116587930,0.9078685880041112
-  "/projects/{projectID}/heatmap/{chromosome}/{region}":
-    get:
-      description: Retrieve local heatmap data
-      operationId: projects_project_id_local_heatmap_data_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-        - name: chromosome
-          in: path
-          description: chromosome number
-          required: true
-          schema:
-            type: string
-          example: "chr1"
-        - name: region
-          in: path
-          description: region number
-          required: true
-          schema:
-            type: string
-          example: "Region1"
-      responses:
-        "200":
-          description: |
-            Local manhattan plot data in CSV format
-          content:
-            text/csv; charset=utf-8:
-              schema:
-                type: string
-                title: Local heatmap plot data
-              example: |
-                ID,rs545945172,rs371628865,rs61769339,rs539032812,rs12238997,rs189800799
-                z_IHEC_MONOP,-0.3623372836601329,-0.429856541533544,-0.8457360635272954,-0.9809852811227732,-0.6936527568935886,0.4382385293216385
-                z_RA_RA,,,,,,
-  "/projects/{projectID}/zoom_manhattan":
-    get:
-      description: Retrieve local manhattan data
-      operationId: projects_project_id_zoom_manhattan_data_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-      responses:
-        "200":
-          description: |
-            Local manhattan plot data in CSV format
-          content:
-            text/csv; charset=utf-8:
-              schema:
-                type: string
-                title: Local manhattan plot data
-              example: |
-                Region,CHR,position,snp_ids,JASS_PVAL
-                Region1,chr1,636285,rs545945172,0.7216577092326355
-                Region1,chr1,662414,rs371628865,0.6725666758876788
-                Region1,chr1,662622,rs61769339,0.405683282952658
-                Region1,chr1,665266,rs539032812,0.3348008598497511
-                Region1,chr1,693731,rs12238997,0.4952464035829177
-                Region1,chr1,701835,rs189800799,0.666563580963709
-                Region1,chr1,706778,rs113462541,0.861641963454806
-                Region1,chr1,711310,rs200531508,0.07463266395489108
-                Region1,chr1,714019,rs114983708,0.6667198743938074
-                Region1,chr1,715265,rs12184267,0.6666055494294745
-                Region1,chr1,715367,rs12184277,0.7657858702655146
-                Region1,chr1,720381,rs116801199,0.6816390671665746
-                Region1,chr1,723742,rs28375378,0.7124933618852456
-                Region1,chr1,724324,rs28692873,0.9212425499680825
-                Region1,chr1,725196,rs377099097,0.594983644175122
-                Region1,chr1,725389,rs375619475,0.7032290172253173
-                Region1,chr1,727841,rs116587930,0.9078685880041112
-  "/projects/{projectID}/zoom_heatmap":
-    get:
-      description: Retrieve local heatmap data
-      operationId: projects_project_id_zoom_heatmap_data_get
-      parameters:
-        - name: projectID
-          in: path
-          description: project ID
-          required: true
-          schema:
-            type: string
-          example: "bca9d414e0f9a67b9e0d2131a47c316c"
-      responses:
-        "200":
-          description: |
-            Local manhattan plot data in CSV format
-          content:
-            text/csv; charset=utf-8:
-              schema:
-                type: string
-                title: Local heatmap plot data
-              example: |
-                ID,rs545945172,rs371628865,rs61769339,rs539032812,rs12238997,rs189800799
-                z_IHEC_MONOP,-0.3623372836601329,-0.429856541533544,-0.8457360635272954,-0.9809852811227732,-0.6936527568935886,0.4382385293216385
-                z_RA_RA,,,,,,
-components:
-  schemas:
-    Phenotype:
-      properties:
-        id:
-          type: string
-        consortium:
-          type: string
-        outcome:
-          type: string
-        full_name:
-          type: string
-        type:
-          type: string
-        ref:
-          type: string
-        ref_link:
-          type: string
-        data_link:
-          type: string
-        data_path:
-          type: string
-    Project:
-      properties:
-        id:
-          type: string
-        status:
-          type: string
-        progress:
-          type: string
-        outcome:
-          type: array
-          items:
-            $ref: "#/components/schemas/Phenotype"
-
+openapi: 3.0.0
+info:
+  version: 0.0.0
+  title: JASS API Specification
+paths:
+  /phenotypes:
+    get:
+      description: |
+        Gets the list of available phenotypes
+      operationId: phenotypes_get
+      responses:
+        "200":
+          description: List of the available phenotypes
+          content:
+            "application/json":
+              schema:
+                type: array
+                title: ArrayOfPhenotypes
+                items:
+                  $ref: "#/components/schemas/Phenotype"
+              example:
+                - "consortium": "IHEC"
+                  "data_link": "http://www.bloodcellgenetics.org"
+                  "full_name": "Monocyte percentage of white cells"
+                  "id": "z_IHEC_MONOP"
+                  "outcome": "MONOP"
+                  "ref": " Astle et al. 2016"
+                  "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/27863262"
+                  "type": "Cellular"
+                - "consortium": "RA"
+                  "data_link": "http://plaza.umin.ac.jp/~yokada/datasource/software.htm"
+                  "full_name": "Rheumatoid Arthritis"
+                  "id": "z_RA_RA"
+                  "outcome": "RA"
+                  "ref": "Okada et al. 2014"
+                  "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/24390342"
+                  "type": "Immunity"
+  /projects:
+    post:
+      description: |
+        Create a new project from a selection of phenotypes
+      operationId: projects_post
+      requestBody:
+        content:
+          application/x-www-form-urlencoded:
+            schema:
+              type: object
+              properties:
+                phenotypeID:
+                  description: IDs of the phenotypes selected for the project
+                  type: array
+                  items:
+                    type: string
+              required:
+                - phenotypeID
+            example:
+              - z_IHEC_MONOP
+              - z_RA_RA
+      responses:
+        "200":
+          description: Project created
+          content:
+            "application/json":
+              schema:
+                $ref: "#/components/schemas/Phenotype"
+              examples:
+                Creating:
+                  value:
+                    id: "bca9d414e0f9a67b9e0d2131a47c316c"
+                    phenotypes:
+                      - "consortium": "IHEC"
+                        "data_link": "http://www.bloodcellgenetics.org"
+                        "full_name": "Monocyte percentage of white cells"
+                        "id": "z_IHEC_MONOP"
+                        "outcome": "MONOP"
+                        "ref": " Astle et al. 2016"
+                        "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/27863262"
+                        "type": "Cellular"
+                      - "consortium": "RA"
+                        "data_link": "http://plaza.umin.ac.jp/~yokada/datasource/software.htm"
+                        "full_name": "Rheumatoid Arthritis"
+                        "id": "z_RA_RA"
+                        "outcome": "RA"
+                        "ref": "Okada et al. 2014"
+                        "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/24390342"
+                        "type": "Immunity"
+                    status":
+                      "global_manhattan": "CREATING"
+                      "quadrant_plot_status": "CREATING"
+                      "worktable": "CREATING"
+                    progress":
+                      "progress": "0"
+                Ready:
+                  value:
+                    id: "bca9d414e0f9a67b9e0d2131a47c316c"
+                    phenotypes:
+                      - "consortium": "IHEC"
+                        "data_link": "http://www.bloodcellgenetics.org"
+                        "full_name": "Monocyte percentage of white cells"
+                        "id": "z_IHEC_MONOP"
+                        "outcome": "MONOP"
+                        "ref": " Astle et al. 2016"
+                        "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/27863262"
+                        "type": "Cellular"
+                      - "consortium": "RA"
+                        "data_link": "http://plaza.umin.ac.jp/~yokada/datasource/software.htm"
+                        "full_name": "Rheumatoid Arthritis"
+                        "id": "z_RA_RA"
+                        "outcome": "RA"
+                        "ref": "Okada et al. 2014"
+                        "ref_link": "https://www.ncbi.nlm.nih.gov/pubmed/24390342"
+                        "type": "Immunity"
+                    status":
+                      "global_manhattan": "READY"
+                      "quadrant_plot_status": "READY"
+                      "worktable": "READY"
+                    progress":
+                      "progress": "100"
+  /local_project:
+    post:
+      description: |
+        Create a new local project from a selection of phenotypes
+      operationId: local_project_post
+      requestBody:
+        content:
+          application/x-www-form-urlencoded:
+            schema:
+              type: object
+              properties:
+                phenotypeID:
+                  description: IDs of the phenotypes selected for the project
+                  type: array
+                  items:
+                    type: string
+                chromosome:
+                  description: chromosome number
+                  type: string
+                start:
+                  description: start position of the region
+                  type: string
+                end:
+                  description: end position of the region
+                  type: string
+              required:
+                - phenotypeID
+                - chromosome
+                - start
+                - end
+      responses:
+        "200":
+          description: Project created
+          content:
+            "application/json":
+              schema:
+                $ref: "#/components/schemas/Phenotype"
+  "/projects/{projectID}":
+    get:
+      description: |
+        Retrieve a project definition
+      operationId: projects_project_idget
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+      responses:
+        "200":
+          description: Retrieved project
+          content:
+            "application/json":
+              schema:
+                $ref: "#/components/schemas/Phenotype"
+              example:
+                id: "bca9d414e0f9a67b9e0d2131a47c316c"
+                status":
+                  "global_manhattan": "READY"
+                  "quadrant_plot_status": "READY"
+                  "worktable": "READY"
+                progress":
+                  "progress": "100"
+  "/projects/{projectID}/summary":
+    get:
+      description: Retrieve summary statistics for a given project
+      operationId: projects_project_id_summary_statistics
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+      responses:
+        "200":
+          description: Summary statistics in JSON
+          content:
+            "*/*":
+              schema:
+                type: string
+                title: Project summary statistics
+              example:
+                "JOSTSignif":
+                  "NoPhenoSignif": 10
+                  "PhenoSignif": 210
+                "NoJOSTSignif":
+                  "NoPhenoSignif": 1470
+                  "PhenoSignif": 14
+  "/projects/{projectID}/csv_status":
+    get:
+      description: |
+        Retrieve the generation status of the genome full csv file
+      operationId: projects_project_id_csv_status_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+      responses:
+        "200":
+          description: |
+            Generation status of the genome full csv file
+          content:
+            text/csv; charset=utf-8:
+              schema:
+                type: string
+                title: csv_file_generation
+              example: |
+                READY
+  "/projects/{projectID}/genome":
+    get:
+      description: |
+        Retrieve whole genome summary data for a given project
+      operationId: projects_project_id_genome_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+      responses:
+        "200":
+          description: |
+            Whole genome summary data in CSV format
+          content:
+            text/csv; charset=utf-8:
+              schema:
+                type: string
+                title: Genome data
+              example: |
+                Region,MiddlePosition,snp_ids,CHR,position,Ref_allele,Alt_allele,JOSTmin,UNIVARIATE_MIN_PVAL,signif_status,z_IHEC_MONOP,z_RA_RA
+                Region0,0.0,rs61997853,chr15,20001087,C,A,0.3085010612493116,0.300300000000003,None,-1.0357902654077036,
+                Region1,951595.0,rs28635530,chr1,1649392,T,C,4.038788020606384e-06,2.7559999999999873e-06,None,4.688213804974398,2.999976992703393
+                Region2,2737671.5,rs72644697,chr1,2533605,A,G,2.4600636176583336e-10,1.6188949607934016e-10,Both,-1.4356568827860683,-6.393727818324495
+                Region3,3981773.5,rs12145992,chr1,3760309,A,G,0.0002538976722549933,0.00026034845141981964,None,-1.6164363711150218,3.651859369008055
+                Region4,5147352.0,rs2649072,chr1,5754088,G,A,0.0007863952492527496,0.0006378999999999985,None,3.4149658871961184,-2.999976992703393
+                Region5,6580614.0,rs2986741,chr1,6548774,G,A,0.0013472918321710914,0.0011119999999999993,None,-3.260540717377886,2.726551316504396
+                Region6,8306267.0,rs79412885,chr1,9241839,A,G,2.0889091093474285e-13,8.106999999999937e-14,Both,7.46857160133221,-1.2003588580308502
+                Region7,10086091.5,rs113829298,chr1,10061038,T,C,4.3158209846991565e-05,6.135999999999996e-06,None,-4.5216481219798474,0.5100734569685951
+  "/projects/{projectID}/genome_full":
+    get:
+      description: |
+        Retrieve whole genome complete (not summarized) data for a given project
+      operationId: projects_project_id_genome_full_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+      responses:
+        "200":
+          description: >
+            Retrieve whole genome complete (not summarized) data for a given
+            project in CSV format
+          content:
+            text/csv; charset=utf-8:
+              schema:
+                type: string
+                title: Genome data
+              example: |
+                Region,CHR,snp_ids,position,Ref_allele,Alt_allele,MiddlePosition,JASS_PVAL,UNIVARIATE_MIN_PVAL,UNIVARIATE_MIN_QVAL,PLEIOTROPY_INDEX,z_IHEC_MONOP,z_RA_RA
+                194218,0,6,rs530120680,63980,G,A,0.0,0.6556994470547299,0.6501999999999999,0.6501999999999999,,0.4534843639637209,
+                194219,0,6,rs561313667,63979,T,C,0.0,0.538722344719537,0.5318,0.5318,,0.6252606526209208,
+                194220,0,15,rs113772187,20000538,T,C,0.0,0.5218942699938458,0.5148000000000001,0.5148000000000001,,-0.651381887083556,
+                194221,0,15,rs61997852,20001079,C,A,0.0,0.33819737748654505,0.33000000000000274,0.33000000000000274,,-0.9741138770593036,
+                194222,0,15,rs61997853,20001087,C,A,0.0,0.3085010612493116,0.300300000000003,0.300300000000003,,-1.0357902654077036,
+                867,1,1,rs10454464,1833495,A,G,951595.0,0.2523888759643953,0.19000000000000383,0.38000000000000766,,-0.9817967289175548,1.3105791121681174
+                4836,1,1,rs10907175,1130727,C,A,951595.0,0.3313846158840952,0.21180000000000354,0.4236000000000071,,1.2486311872236304,0.8380752842791193
+                4837,1,1,rs10907176,1130855,C,T,951595.0,0.3455642965805482,0.2251000000000033,0.4502000000000066,,1.213078000845954,0.8380752842791193
+                4838,1,1,rs10907185,1733219,A,G,951595.0,0.3919109214945312,0.25000000000000333,0.5000000000000067,,-0.7010048315295425,1.1503493803760003
+                4839,1,1,rs10907187,1759054,A,G,951595.0,0.16161974795348924,0.09099999999999998,0.18199999999999997,,-0.8114627085037827,1.6901461375274702
+                4840,1,1,rs10907188,1768894,T,C,951595.0,0.15366147518120524,0.08599999999999992,0.17199999999999985,,-0.8149516264832889,1.7168860184310413
+                4841,1,1,rs10907190,1773772,A,G,951595.0,0.12979175667585227,0.07999999999999982,0.15999999999999964,,-0.938281041511616,1.7506860712521708
+                4842,1,1,rs10907193,1805391,A,G,951595.0,0.09562672355608258,0.06299999999999988,0.12599999999999975,,-1.0405165049626888,1.8591914944718688
+                4843,1,1,rs10907194,1712230,T,C,951595.0,0.2669995168398967,0.16000000000000425,0.3200000000000085,,-0.7600913211933399,1.4050715603096189
+  "/projects/{projectID}/globalmanhattan":
+    get:
+      description: |
+        Retrieve global manhattan plot for a given project
+      operationId: projects_project_id_global_manhattan_plot_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+      responses:
+        "200":
+          description: |
+            Global manhattan plot in PNG format
+          content:
+            image/png:
+              schema:
+                type: string
+                title: Global manhattan plot
+              example:
+                externalValue: "globalmanhattan_example.png"
+  "/projects/{projectID}/zoomplot":
+    get:
+      description: |
+        Retrieve zoom plot for a given local project
+      operationId: projects_project_id_zoom_plot_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+      responses:
+        "200":
+          description: |
+            Zoom plot in PNG format
+          content:
+            image/png:
+              schema:
+                type: string
+                title: Zoom plot
+  "/projects/{projectID}/quadrant":
+    get:
+      description: |
+        Retrieve quadrant plot for a given project
+      operationId: projects_project_id_quadrant_plot_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+      responses:
+        "200":
+          description: |
+            Quadrant plot in PNG format
+          content:
+            image/png:
+              schema:
+                type: string
+                title: Quadrant plot
+              example:
+                externalValue: "quadrant_example.png"
+  "/projects/{projectID}/manhattan/{chromosome}/{region}":
+    get:
+      description: Retrieve local manhattan data
+      operationId: projects_project_id_local_manhattan_data_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+        - name: chromosome
+          in: path
+          description: chromosome number
+          required: true
+          schema:
+            type: string
+          example: "chr1"
+        - name: region
+          in: path
+          description: region number
+          required: true
+          schema:
+            type: string
+          example: "Region1"
+      responses:
+        "200":
+          description: |
+            Local manhattan plot data in CSV format
+          content:
+            text/csv; charset=utf-8:
+              schema:
+                type: string
+                title: Local manhattan plot data
+              example: |
+                Region,CHR,position,snp_ids,JASS_PVAL
+                Region1,chr1,636285,rs545945172,0.7216577092326355
+                Region1,chr1,662414,rs371628865,0.6725666758876788
+                Region1,chr1,662622,rs61769339,0.405683282952658
+                Region1,chr1,665266,rs539032812,0.3348008598497511
+                Region1,chr1,693731,rs12238997,0.4952464035829177
+                Region1,chr1,701835,rs189800799,0.666563580963709
+                Region1,chr1,706778,rs113462541,0.861641963454806
+                Region1,chr1,711310,rs200531508,0.07463266395489108
+                Region1,chr1,714019,rs114983708,0.6667198743938074
+                Region1,chr1,715265,rs12184267,0.6666055494294745
+                Region1,chr1,715367,rs12184277,0.7657858702655146
+                Region1,chr1,720381,rs116801199,0.6816390671665746
+                Region1,chr1,723742,rs28375378,0.7124933618852456
+                Region1,chr1,724324,rs28692873,0.9212425499680825
+                Region1,chr1,725196,rs377099097,0.594983644175122
+                Region1,chr1,725389,rs375619475,0.7032290172253173
+                Region1,chr1,727841,rs116587930,0.9078685880041112
+  "/projects/{projectID}/heatmap/{chromosome}/{region}":
+    get:
+      description: Retrieve local heatmap data
+      operationId: projects_project_id_local_heatmap_data_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+        - name: chromosome
+          in: path
+          description: chromosome number
+          required: true
+          schema:
+            type: string
+          example: "chr1"
+        - name: region
+          in: path
+          description: region number
+          required: true
+          schema:
+            type: string
+          example: "Region1"
+      responses:
+        "200":
+          description: |
+            Local manhattan plot data in CSV format
+          content:
+            text/csv; charset=utf-8:
+              schema:
+                type: string
+                title: Local heatmap plot data
+              example: |
+                ID,rs545945172,rs371628865,rs61769339,rs539032812,rs12238997,rs189800799
+                z_IHEC_MONOP,-0.3623372836601329,-0.429856541533544,-0.8457360635272954,-0.9809852811227732,-0.6936527568935886,0.4382385293216385
+                z_RA_RA,,,,,,
+  "/projects/{projectID}/zoom_manhattan":
+    get:
+      description: Retrieve local manhattan data
+      operationId: projects_project_id_zoom_manhattan_data_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+      responses:
+        "200":
+          description: |
+            Local manhattan plot data in CSV format
+          content:
+            text/csv; charset=utf-8:
+              schema:
+                type: string
+                title: Local manhattan plot data
+              example: |
+                Region,CHR,position,snp_ids,JASS_PVAL
+                Region1,chr1,636285,rs545945172,0.7216577092326355
+                Region1,chr1,662414,rs371628865,0.6725666758876788
+                Region1,chr1,662622,rs61769339,0.405683282952658
+                Region1,chr1,665266,rs539032812,0.3348008598497511
+                Region1,chr1,693731,rs12238997,0.4952464035829177
+                Region1,chr1,701835,rs189800799,0.666563580963709
+                Region1,chr1,706778,rs113462541,0.861641963454806
+                Region1,chr1,711310,rs200531508,0.07463266395489108
+                Region1,chr1,714019,rs114983708,0.6667198743938074
+                Region1,chr1,715265,rs12184267,0.6666055494294745
+                Region1,chr1,715367,rs12184277,0.7657858702655146
+                Region1,chr1,720381,rs116801199,0.6816390671665746
+                Region1,chr1,723742,rs28375378,0.7124933618852456
+                Region1,chr1,724324,rs28692873,0.9212425499680825
+                Region1,chr1,725196,rs377099097,0.594983644175122
+                Region1,chr1,725389,rs375619475,0.7032290172253173
+                Region1,chr1,727841,rs116587930,0.9078685880041112
+  "/projects/{projectID}/zoom_heatmap":
+    get:
+      description: Retrieve local heatmap data
+      operationId: projects_project_id_zoom_heatmap_data_get
+      parameters:
+        - name: projectID
+          in: path
+          description: project ID
+          required: true
+          schema:
+            type: string
+          example: "bca9d414e0f9a67b9e0d2131a47c316c"
+      responses:
+        "200":
+          description: |
+            Local manhattan plot data in CSV format
+          content:
+            text/csv; charset=utf-8:
+              schema:
+                type: string
+                title: Local heatmap plot data
+              example: |
+                ID,rs545945172,rs371628865,rs61769339,rs539032812,rs12238997,rs189800799
+                z_IHEC_MONOP,-0.3623372836601329,-0.429856541533544,-0.8457360635272954,-0.9809852811227732,-0.6936527568935886,0.4382385293216385
+                z_RA_RA,,,,,,
+components:
+  schemas:
+    Phenotype:
+      properties:
+        id:
+          type: string
+        consortium:
+          type: string
+        outcome:
+          type: string
+        full_name:
+          type: string
+        type:
+          type: string
+        ref:
+          type: string
+        ref_link:
+          type: string
+        data_link:
+          type: string
+        data_path:
+          type: string
+    Project:
+      properties:
+        id:
+          type: string
+        status:
+          type: string
+        progress:
+          type: string
+        outcome:
+          type: array
+          items:
+            $ref: "#/components/schemas/Phenotype"
-- 
GitLab


From e8b744656c80d68d61558bf0869cfe3d7f9e76df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Thu, 8 Jul 2021 17:32:35 +0200
Subject: [PATCH 21/25] fix URL endpoints to retrieve phenotypes and launch
 analyses

these endpoints should not end with a slash
---
 jass/server.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/jass/server.py b/jass/server.py
index 9945f24..7d5f045 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -79,7 +79,7 @@ def get_phenotypes():
     return get_available_phenotypes(os.path.join(config["DATA_DIR"], "initTable.hdf5"))
 
 
-@blp_phenotypes.route("/")
+@blp_phenotypes.route("")
 class PhenotypesMethodView(MethodView):
     @blp_phenotypes.response(200, PhenotypeSchema(many=True))
     def get(self):
@@ -87,7 +87,7 @@ class PhenotypesMethodView(MethodView):
         return get_phenotypes()
 
 
-@blp_projects.route("/")
+@blp_projects.route("")
 class ProjectCreateMethodView(MethodView):
     @blp_projects.arguments(ProjectParamsSchema(), location="form")
     @blp_projects.response(200, ProjectSchema())
@@ -102,7 +102,7 @@ class ProjectCreateMethodView(MethodView):
         return create_project([p.id for p in phenotypes], get_phenotypes())
 
 
-@blp_local_projects.route("/")
+@blp_local_projects.route("")
 class LocalProjectCreateMethodView(MethodView):
     @blp_projects.arguments(LocalProjectParamsSchema(), location="form")
     @blp_projects.response(200, ProjectSchema())
-- 
GitLab


From 187de44c21bf69fd19aedfc3fa7a63786cec0340 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Fri, 9 Jul 2021 10:11:30 +0200
Subject: [PATCH 22/25] fix unit tests according to API URLs modifications

---
 jass/test/test_server.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/jass/test/test_server.py b/jass/test/test_server.py
index 9bf088b..8547712 100644
--- a/jass/test/test_server.py
+++ b/jass/test/test_server.py
@@ -19,7 +19,7 @@ class TestDefaultController(JassFlaskTestCase):
         """
         Test case retrieving available phenotypes
         """
-        response = self.testing_client.open("/api/phenotypes/", method="GET")
+        response = self.testing_client.open("/api/phenotypes", method="GET")
         self.assert200(response, "Response body is : " + response.data.decode("utf-8"))
 
     def test_create_project(self):
@@ -27,7 +27,7 @@ class TestDefaultController(JassFlaskTestCase):
         Test case for creating a project
         """
         response = self.testing_client.open(
-            "/api/projects/",
+            "/api/projects",
             method="POST",
             data={"phenotypeID": "z_IHEC_MONOP,z_RA_RA"},
         )
-- 
GitLab


From 85c461f4feb585e82a4cdf804726c3b37c7defa4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@gmail.com>
Date: Sat, 10 Jul 2021 19:14:37 +0200
Subject: [PATCH 23/25] return properly serialized phenotypes to project
 submission/status

many thanks to @cnerin for catching that bug
---
 jass/server.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jass/server.py b/jass/server.py
index 7d5f045..1402643 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -52,7 +52,7 @@ class ProjectStatusSchema(ma.Schema):
 class ProjectSchema(ma.Schema):
     id = ma.fields.String()
     status = ma.fields.Nested(ProjectStatusSchema)
-    phenotypes = ma.fields.List(ma.fields.String())
+    phenotypes = ma.fields.List(ma.fields.Nested(PhenotypeSchema()))
     progress = ma.fields.String()
 
 
-- 
GitLab


From 7a7871f90c66cbe46f102e0b8cf8b69ae7e38df0 Mon Sep 17 00:00:00 2001
From: genstat <cyril.nerin@pasteur.fr>
Date: Sun, 11 Jul 2021 11:36:30 +0200
Subject: [PATCH 24/25] fix #87

---
 jass/server.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/jass/server.py b/jass/server.py
index 1402643..a667b5e 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -176,12 +176,18 @@ class ProjectGenomeMethodView(MethodView):
 @blp_projects.route("/<project_id>/genome_full")
 class ProjectGenomeFullMethodView(MethodView):
     def get(self, project_id):
+        Type_of_Analysis = Project(id=project_id).get_type_of_analysis()
+        if(Type_of_Analysis == Project.LOCAL_ANALYSIS):
+            Fichier = "local_analysis_result.csv"
+        else:
+            Fichier = "genome_full.csv"
+        
         try:
             return send_file(
                 Project(id=project_id).get_csv_path(),
                 mimetype="text/csv",
                 as_attachment=True,
-                attachment_filename="genome_full.csv",
+                attachment_filename=Fichier,
             )
         except FileNotFoundError:
             status = Project(id=project_id).status
-- 
GitLab


From 29adcf61efad49e3a14b30afdbf40af2918b4ec8 Mon Sep 17 00:00:00 2001
From: genstat <cyril.nerin@pasteur.fr>
Date: Sun, 11 Jul 2021 11:36:55 +0200
Subject: [PATCH 25/25] FIX #89

---
 jass/static/directLink.html | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/jass/static/directLink.html b/jass/static/directLink.html
index c645222..926cedf 100644
--- a/jass/static/directLink.html
+++ b/jass/static/directLink.html
@@ -111,10 +111,10 @@
 			}
 		}
 		if (Local_Analysis == true) {
-			var The_Project = "/api/local_project/" + 
-							  chromosome + "/" + 
-							  start + "/" + 
-							  end;
+			phe['chromosome'] = chromosome;
+			phe['start'] = start;
+			phe['end'] = end;
+			var The_Project = "/api/local_projects";
 		}
 		else{
 			var The_Project = "/api/projects";
-- 
GitLab

