Do not use mails for standalone version: make treatments synchronous instead, Fixes #117

src/dgenies/lib/functions.py

@@ -58,7 +58,7 @@ class Functions:
         fasta_file = None
         try:
             with open(os.path.join(res_dir, "." + type_f), "r") as save_name:
-                fasta_file = save_name.readline()
+                fasta_file = save_name.readline().strip("\n")
         except IOError:
             print(res_dir + ": Unable to load saved name for " + type_f, file=sys.stderr)
             pass

src/dgenies/lib/paf.py

 #!/usr/bin/env python3
 
+from dgenies import MODE
+
 import os
 import shutil
 from math import sqrt
@@ -762,12 +764,13 @@ class Paf:
             o_fasta = "_._"
             status="fail"
 
-        parts = os.path.basename(o_fasta).rsplit(".", 1)
-        Functions.send_fasta_ready(mailer=self.mailer,
-                                   job_name=self.id_job,
-                                   sample_name=parts[0],
-                                   ext=parts[1],
-                                   compressed=False,
-                                   path="download",
-                                   status=status)
+        if MODE == "webserver":
+            parts = os.path.basename(o_fasta).rsplit(".", 1)
+            Functions.send_fasta_ready(mailer=self.mailer,
+                                       job_name=self.id_job,
+                                       sample_name=parts[0],
+                                       ext=parts[1],
+                                       compressed=False,
+                                       path="download",
+                                       status=status)
         return o_fasta

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

@@ -34,7 +34,6 @@ dgenies.result.export.export_svg = function () {
         dgenies.result.export.save_file(blob, "svg");
     };
     d3.boxplot.zoom.reset_scale(true, after);
-
 };
 
 dgenies.result.export.export_paf = function () {
@@ -141,7 +140,7 @@ dgenies.result.export.export_no_association_file = function (to) {
         })
 };
 
-dgenies.result.export.export_query_as_reference_fasta = function() {
+dgenies.result.export.export_query_as_reference_fasta_webserver = function() {
     dgenies.post(`/build-query-as-reference/${dgenies.result.id_res}`,
         {},
         function (data, success) {
@@ -149,10 +148,32 @@ dgenies.result.export.export_query_as_reference_fasta = function() {
                 dgenies.notify("You will receive a mail soon with the link to download your Fasta file", "success")
             }
             else {
-                dgenies.notify(`An error has occurred. Please contact the support`, "fatal")
+                dgenies.notify(`An error has occurred. Please contact the support`, "danger")
             }
         });
-}
+};
+
+dgenies.result.export.export_query_as_reference_fasta_standalone = function () {
+    dgenies.show_loading("Building file...", 180);
+    window.setTimeout(() => {
+        dgenies.post(`/build-query-as-reference/${dgenies.result.id_res}`,
+        {},
+        function (data, success) {
+            if (data["success"]) {
+                let export_div = $("div#export-pict");
+                export_div.html("");
+                export_div.append($("<a>").attr("href", `/get-query-as-reference/${dgenies.result.id_res}`)
+                    .attr("download", `as_reference_${d3.boxplot.name_y}.fasta`)
+                    .attr("id", "my-download").text("download"));
+                document.getElementById('my-download').click();
+                dgenies.hide_loading();
+            }
+            else {
+                dgenies.notify(`An error has occurred. Please contact the support`, "danger")
+            }
+        });
+    }, 0);
+};
 
 dgenies.result.export.export = function () {
     let select = $("form#export select");
@@ -180,7 +201,13 @@ dgenies.result.export.export = function () {
                 dgenies.result.export.export_no_association_file("target");
             }
             else if (selection === 8) {
-                dgenies.result.export.export_query_as_reference_fasta();
+                if (dgenies.result.mode === "webserver") {
+                    dgenies.result.export.export_query_as_reference_fasta_webserver();
+                }
+                else {
+                    dgenies.result.export.export_query_as_reference_fasta_standalone();
+                    async = true;
+                }
             }
             else
                 dgenies.notify("Not supported yet!", "danger", 2000);

src/dgenies/views.py

@@ -350,7 +350,7 @@ def build_fasta(id_res):
         if is_sorted and not query_fasta.endswith(".sorted"):
             # Do the sort
             Path(lock_query).touch()
-            if not compressed:  # If compressed, it will took a long time, so not wait
+            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,
@@ -361,17 +361,17 @@ def build_fasta(id_res):
                 "mailer": mailer
             })
             thread.start()
-            if not compressed:
+            if not compressed or MODE == "standalone":
                 i = 0
                 time.sleep(5)
-                while os.path.exists(lock_query) and i < 2:
+                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"})
                 return jsonify({"success": True, "status": 2, "status_message": "Done",
-                                "gzip": False})
+                                "gzip": compressed})
             else:
                 return jsonify({"success": True, "status": 1, "status_message": "In progress"})
         elif is_sorted and os.path.exists(lock_query):
@@ -399,18 +399,32 @@ def build_fasta(id_res):
                         "message": "Unable to get fasta file for query. Please contact us to report the bug"})
 
 
-@app.route('/build-query-as-reference/<id_res>', methods=['POST'])
-def get_query_as_reference(id_res):
+def build_query_as_reference(id_res):
     paf_file = os.path.join(APP_DATA, id_res, "map.paf")
     idx1 = os.path.join(APP_DATA, id_res, "query.idx")
     idx2 = os.path.join(APP_DATA, id_res, "target.idx")
     paf = Paf(paf_file, idx1, idx2, False, mailer=mailer, id_job=id_res)
     paf.parse_paf(False, True)
-    thread = threading.Timer(0, paf.build_query_chr_as_reference)
-    thread.start()
+    if MODE == "webserver":
+        thread = threading.Timer(0, paf.build_query_chr_as_reference)
+        thread.start()
+        return True
+    return paf.build_query_chr_as_reference()
+
+
+@app.route('/build-query-as-reference/<id_res>', methods=['POST'])
+def post_query_as_reference(id_res):
+    build_query_as_reference(id_res)
     return jsonify({"success": True})
 
 
+@app.route('/get-query-as-reference/<id_res>', methods=['GET'])
+def get_query_as_reference(id_res):
+    if MODE != "standalone":
+        return abort(404)
+    return send_file(build_query_as_reference(id_res))
+
+
 @app.route('/download/<id_res>/<filename>')
 def download_file(id_res, filename):
     file_dl = os.path.join(APP_DATA, id_res, filename)