Don't ask for compression on standalone mode + fix bug on windows

src/dgenies/lib/functions.py

@@ -161,7 +161,7 @@ class Functions:
 
 
     @staticmethod
-    def sort_fasta(job_name, fasta_file, index_file, lock_file, compress=False, mailer=None):
+    def sort_fasta(job_name, fasta_file, index_file, lock_file, compress=False, mailer=None, mode="webserver"):
         index, sample_name = Functions.read_index(index_file)
         is_compressed = fasta_file.endswith(".gz")
         if is_compressed:
@@ -185,7 +185,7 @@ class Functions:
         if compress:
             Functions.compress(fasta_file_o)
         os.remove(lock_file)
-        if mailer is not None and not os.path.exists(lock_file + ".pending"):
+        if mode == "webserver" and mailer is not None and not os.path.exists(lock_file + ".pending"):
             Functions.send_fasta_ready(mailer, job_name, sample_name, compress)
 
     @staticmethod

src/dgenies/static/js/dgenies.result.export.js

@@ -86,36 +86,41 @@ dgenies.result.export.export_fasta = function(compress=false) {
 };
 
 dgenies.result.export.ask_export_fasta = function () {
-    let dialog = $("<div>")
-        .attr("id", "dialog-confirm")
-        .attr("title", "Gzip?");
-    let icon = $("<span>")
-        .attr("class", "ui-icon ui-icon-help")
-        .css("float", "left")
-        .css("margin", "12px 12px 20px 0");
-    let body = $("<p>");
-    body.append(icon);
-    body.append("Compression is recommanded on slow connections. Download Gzip file?");
-    dialog.append(body);
-    dialog.dialog({
-        resizable: false,
-        height: "auto",
-        width: 500,
-        modal: true,
-        buttons: {
-            "Use default": function() {
-                $( this ).dialog( "close" );
-                dgenies.result.export.export_fasta(false);
-            },
-            "Use Gzip": function () {
-                $( this ).dialog( "close" );
-                dgenies.result.export.export_fasta(true);
-            },
-            Cancel: function () {
-                $( this ).dialog( "close" );
+    if (dgenies.mode === "webserver") {
+        let dialog = $("<div>")
+            .attr("id", "dialog-confirm")
+            .attr("title", "Gzip?");
+        let icon = $("<span>")
+            .attr("class", "ui-icon ui-icon-help")
+            .css("float", "left")
+            .css("margin", "12px 12px 20px 0");
+        let body = $("<p>");
+        body.append(icon);
+        body.append("Compression is recommanded on slow connections. Download Gzip file?");
+        dialog.append(body);
+        dialog.dialog({
+            resizable: false,
+            height: "auto",
+            width: 500,
+            modal: true,
+            buttons: {
+                "Use default": function () {
+                    $(this).dialog("close");
+                    dgenies.result.export.export_fasta(false);
+                },
+                "Use Gzip": function () {
+                    $(this).dialog("close");
+                    dgenies.result.export.export_fasta(true);
+                },
+                Cancel: function () {
+                    $(this).dialog("close");
+                }
             }
-        }
-    });
+        });
+    }
+    else {
+        dgenies.result.export.export_fasta(false);
+    }
 };
 
 dgenies.result.export.export_association_table = function () {

src/dgenies/views.py

@@ -391,21 +391,33 @@ def build_fasta(id_res):
             Path(lock_query).touch()
             if not compressed or MODE == "standalone":  # If compressed, it will took a long time, so not wait
                 Path(lock_query + ".pending").touch()
-            thread = threading.Timer(1, Functions.sort_fasta, kwargs={
-                "job_name": id_res,
-                "fasta_file": query_fasta,
-                "index_file": os.path.join(res_dir, "query.idx.sorted"),
-                "lock_file": lock_query,
-                "compress": compressed,
-                "mailer": mailer
-            })
-            thread.start()
+            index_file = os.path.join(res_dir, "query.idx.sorted")
+            if MODE == "webserver":
+                thread = threading.Timer(1, Functions.sort_fasta, kwargs={
+                    "job_name": id_res,
+                    "fasta_file": query_fasta,
+                    "index_file": index_file,
+                    "lock_file": lock_query,
+                    "compress": compressed,
+                    "mailer": mailer,
+                    "mode": MODE
+                })
+                thread.start()
+            else:
+                Functions.sort_fasta(job_name=id_res,
+                                     fasta_file=query_fasta,
+                                     index_file=index_file,
+                                     lock_file=lock_query,
+                                     compress=compressed,
+                                     mailer=None,
+                                     mode=MODE)
             if not compressed or MODE == "standalone":
-                i = 0
-                time.sleep(5)
-                while os.path.exists(lock_query) and (i < 2 or MODE == "standalone"):
-                    i += 1
+                if MODE == "webserver":
+                    i = 0
                     time.sleep(5)
+                    while os.path.exists(lock_query) and (i < 2 or MODE == "standalone"):
+                        i += 1
+                        time.sleep(5)
                 os.remove(lock_query + ".pending")
                 if os.path.exists(lock_query):
                     return jsonify({"success": True, "status": 1, "status_message": "In progress"})