Prevent timeout for summary, Fixes #111

src/dgenies/lib/paf.py

@@ -478,16 +478,12 @@ class Paf:
                     contigs_list.remove(c_name)
         return "\n".join(contigs_list) + "\n"
 
-    def get_summary_stats(self):
+    def build_summary_stats(self, status_file):
         """
         Get summary of identity
         :return: table with percents by category
         """
         summary_file = self.paf + ".summary"
-        if os.path.exists(summary_file):
-            with open(summary_file, "r") as summary_file:
-                txt = summary_file.read()
-                return json.loads(txt)
         self.parse_paf(False, False)
         if self.parsed:
             percents = {}
@@ -509,5 +505,15 @@ class Paf:
             with open(summary_file, "w") as summary_file:
                 summary_file.write(json.dumps(percents))
 
+            os.remove(status_file)
             return percents
+        shutil.move(status_file, status_file + ".fail")
+        return None
+
+    def get_summary_stats(self):
+        summary_file = self.paf + ".summary"
+        if os.path.exists(summary_file):
+            with open(summary_file, "r") as summary_file:
+                txt = summary_file.read()
+                return json.loads(txt)
         return None

src/dgenies/static/js/dgenies.result.controls.js

@@ -19,7 +19,12 @@ dgenies.result.controls.summary = function () {
             function (data) {
                 dgenies.hide_loading();
                 if (data["success"]) {
-                    dgenies.result.summary.show(data["percents"]);
+                    if (data["status"] === "done") {
+                        dgenies.result.summary.show(data["percents"]);
+                    }
+                    else if (data["status"] === "waiting") {
+                        dgenies.result.controls.summary();
+                    }
                 }
                 else {
                     dgenies.notify(data["message"] || "An error occurred! Please contact us to report the bug", "danger");

src/dgenies/views.py

@@ -405,15 +405,44 @@ def summary(id_res):
             "success": False,
             "message": "Unable to load data!"
         })
-    percents = paf.get_summary_stats()
-    if percents is None:
+    percents = None
+    s_status = "waiting"  # Accepted values: waiting, done, fail
+    status_file = os.path.join(APP_DATA, id_res, ".summarize")
+    fail_file = status_file + ".fail"
+    if not os.path.exists(status_file):  # The job is finished or not started
+        if not os.path.exists(fail_file):  # The job has not started yet or has successfully ended
+            percents = paf.get_summary_stats()
+            if percents is None:  # The job has not started yet
+                Path(status_file).touch()
+                thread = threading.Timer(0, paf.build_summary_stats, kwargs={"status_file": status_file})
+                thread.start()
+            else:  # The job has successfully ended
+                s_status = "done"
+        else:  # The job has failed
+            s_status = "fail"
+
+    if s_status == "waiting":  # The job is running
+        # Check if the job end in the next 30 seconds
+        nb_iter = 0
+        while os.path.exists(status_file) and not os.path.exists(fail_file) and nb_iter < 10:
+            time.sleep(3)
+            nb_iter += 1
+        if not os.path.exists(status_file):  # The job has ended
+            percents = paf.get_summary_stats()
+            if percents is None:  # The job has failed
+                s_status = "fail"
+            else:  # The job has successfully ended
+                s_status = "done"
+
+    if s_status == "fail":
         return jsonify({
             "success": False,
             "message": "Build of summary failed. Please contact us to report the bug"
         })
     return jsonify({
         "success": True,
-        "percents": percents
+        "percents": percents,
+        "status": s_status
     })