diff --git a/jass/__main__.py b/jass/__main__.py
index 78f40102ef431e7e8fcc862e9a3022ce32f1ac59..743b290525e685bba88ef410b2283158cebfc795 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
@@ -72,17 +72,17 @@ 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)
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
+ 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("--remove-nans", action="store_true", default=False)
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("--remove-nans", action="store_true", default=False)
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
diff --git a/jass/static/chromo_heatmap_manhattan.html b/jass/static/chromo_heatmap_manhattan.html
index a21806c484ab3f76d33304263cb4f4ed04678e04..dbaceaa54e1bfc1dff96f19f0d8fe2633dc6a631 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>
diff --git a/jass/static/directLink.html b/jass/static/directLink.html
index cb711926e697bf5657ba78376b4a9fd86534eeb3..bad989df75dfc7f8ca6cfcc305296ba306d52d74 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 = "ð–ð€ð‘ððˆðð†: ðð¥ðžðšð¬ðž ðœð¡ð¨ð¨ð¬ðž ðšð§ ðšð«ð«ðšð² ð¨ðŸ ðð¡ðžð§ð¨ðð²ð©ðžð¬..."
+ alert(User_Message);
+ toApply = 0;
+ }
+ else if (selectedNumber == 1){
+ // A confirmation window is displayed
+ var User_Message = "ð–ð€ð‘ððˆðð†: ð²ð¨ð® ð¡ðšð¯ðž ð¬ðžð¥ðžðœððžð ð¨ð§ð¥ð² ð¨ð§ðž ð©ð¡ðžð§ð¨ðð²ð©ðž!" +
+ "\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 = "ð–ð€ð‘ððˆðð†: ð²ð¨ð® ð¡ðšð¯ðž ð¬ðžð¥ðžðœððžð " +
+ selectedNumber +
+ " ð©ð¡ðžð§ð¨ðð²ð©ðžð¬!\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 = "ð„ð‘ð‘ðŽð‘: ð²ð¨ð® ð¡ðšð¯ðž ð¬ðžð¥ðžðœððžð " +
+ selectedNumber +
+ " ð©ð¡ðžð§ð¨ðð²ð©ðžð¬!\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 = "ð–ð€ð‘ððˆðð†: ðð¥ðžðšð¬ðž ðœð¡ð¨ð¨ð¬ðž ðšð§ ðšð«ð«ðšð² ð¨ðŸ ðð¡ðžð§ð¨ðð²ð©ðžð¬..."
+ 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>
diff --git a/jass/static/export.html b/jass/static/export.html
index 23f4666b72eb6bf6d26d8426d51d766dd5402908..969381cf664b7e8eebfdc6e45bbe80641e6f2c1c 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 = $('#pheTable').dataTable( {
+
+ aoColumns: tmpArray,
+ dom: 'Bfrtip',
+ buttons: [ {
+ extend: 'csv',
+
+ text : 'Export to CSV',
+
+ filename: function(){
+
+ var d = new Date();
+
+ var n = d.getTime();
+
+ return 'Data_Table';
+
+ },
+ }]
+
+ } );
+
+ }
+
+
+
+ </script>
+</head>
+
+<body>
+
+<div class="header" > </div>
+
+<h2>Data Table Export</h2>
+
+<div id='divContainer' width ="400px">
+ <table id ="pheTable" style="width :500px" class="display dataTable"></table>
+</div>
+
+</body>
+
+</html>
diff --git a/jass/static/index.html b/jass/static/index.html
index 9f514a80e06a7bdf2aadcbef436a30d13ac534a9..07cbf37ca6e3dac44636de1216733aa87d97efe0 100644
--- a/jass/static/index.html
+++ b/jass/static/index.html
@@ -55,15 +55,15 @@
<div id="tabs-3">
<p><b>JASS: command line and web interface for the joint analysis of GWAS results</b><br />
Hanna Julienne, Pierre Lechat, Vincent Guillemot, Carla Lasry, Chunzi Yao, Robinson Araud, Vincent Laville, Bjarni Vilhjalmsson, Hervé Ménager, Hugues Aschard<br />
- in: NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa003, <a href="https://doi.org/10.1093/nargab/lqaa003"> <FONT color=#0000FF>https://doi.org/10.1093/nargab/lqaa003</FONT></a></p>
+ in: NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa003, <a href="https://urldefense.com/v3/__https://doi.org/10.1093/nargab/lqaa003__;!!JFdNOqOXpB6UZW0!75infPACk5lQWcBTD-rE5FQb6Yk4WckKROxH7a5qa4ERTDyiliWfWLGe8-HIgjvh3Gk$"> <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>
diff --git a/jass/static/selectPhenotypes.html b/jass/static/selectPhenotypes.html
index a49e381e85e5cca9b2f540591b1c3794aa740116..397172271037e33d282caee59a2668c261ea44a9 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"){
diff --git a/requirements.txt b/requirements.txt
index 4d1144be057841f4254e45ba33590528b14d5f21..25400d93c0388519cea98149d04e2cacbade82a3 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 42e05c541211ed485a6e57202e84206b1bc85da4..19675e52aa5d51210c488a360066df4de0043581 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,