Some config refactoring + minor fixes

application.properties

@@ -13,12 +13,18 @@ web_url = http://localhost:5000
 # Please set the unit: M for Megabyte or G for Gigabyte (-1 without unit to don't set a limit)
 max_upload_size = 3G
 # Max upload file size for all-vs-all (only target):
+# Please set the unit: M for Megabyte or G for Gigabyte (-1 without unit to don't set a limit)
 max_upload_size_ava = 1G
 # Max upload file size (compressed or not, only for uploaded files, not from URL):
 # Please set the unit: M for Megabyte or G for Gigabyte (-1 without unit to don't set a limit)
 max_upload_file_size = 1G
 
 
+[softwares]
+minimap2 = ###DEFAULT###
+minimap2_cluster = ###DEFAULT###
+
+
 [debug]
 # Debug (enable only for tests)
 enable = False
@@ -49,7 +55,7 @@ min_query_size = 500M
 min_target_size = 700M
 
 prepare_script = ###PROGRAM###/bin/all_prepare.py
-python3_script = python3
+python3_exec = python3
 # Max memory:
 memory = 32
 # Max memory for all-vs-all mode:
@@ -57,16 +63,11 @@ memory_ava = 32
 threads = 4
 
 
-[softwares]
-minimap2 = ###DEFAULT###
-minimap2_cluster = ###DEFAULT###
-
-
 [database]
 type = sqlite
 url = ###USER###/.dgenies/database.sqlite
 # Not used for sqlite:
-port =
+port = 3306
 db =
 user =
 password =
@@ -82,9 +83,9 @@ send_mail_status = True
 [cron]
 ### Menage
 # Time to launch the cron:
-menage_hour = 1h00
+clean_time = 1h00
 # Frequency (days):
-menage_freq = 1
+clean_freq = 1
 
 
 [jobs]

requirements.txt

@@ -13,3 +13,4 @@ tendo==0.2.*
 matplotlib==2.1.*
 drmaa==0.7.*
 intervaltree==2.1.*
+argparse==1.4

src/dgenies/config_reader.py

@@ -242,21 +242,21 @@ class AppConfigReader:
         except NoOptionError:
             return False
 
-    def _get_cron_menage_hour(self):
+    def _get_cron_clean_time(self):
         try:
-            value = self.reader.get("cron", "menage_hour").lower()
+            value = self.reader.get("cron", "clean_time").lower()
             match = re.match(r"(([0-9])|([0-1][0-9])|(2[0-3]))[hH]([0-5][0-9])", value)
             if match is not None:
                 return [int(match.group(1)), int(match.group(5))]
             else:
-                print("Incorrect menage hour format!")
+                print("Incorrect clean hour format!")
                 return [1, 0]
         except (NoOptionError, NoSectionError):
             return [1, 0]
 
-    def _get_cron_menage_freq(self):
+    def _get_cron_clean_freq(self):
         try:
-            return int(self.reader.get("cron", "menage_freq"))
+            return int(self.reader.get("cron", "clean_freq"))
         except (NoOptionError, NoSectionError):
             return 1
 
@@ -341,9 +341,9 @@ class AppConfigReader:
         except (NoOptionError, NoSectionError):
             return self._replace_vars("###PROGRAM###/bin/prepare_data.sh")
 
-    def _get_cluster_python_script(self):
+    def _get_cluster_python_exec(self):
         try:
-            return self._replace_vars(self.reader.get("cluster", "python3_script"))
+            return self._replace_vars(self.reader.get("cluster", "python3_exec"))
         except (NoOptionError, NoSectionError):
             return "python3"
 

src/dgenies/lib/crons.py

@@ -31,22 +31,22 @@ class Crons:
 
     def start_all(self):
         self.clear(False)
-        self.init_menage_cron()
+        self.init_clean_cron()
         self.init_launch_local_cron()
 
-    def init_menage_cron(self):
+    def init_clean_cron(self):
         """
-        Menage cron is launched at 1h00am each day
+        Clean cron is launched at 1h00am each day
         """
-        menage_hour = self.config.cron_menage_hour
-        menage_freq = self.config.cron_menage_freq
+        clean_time = self.config.cron_clean_time
+        clean_freq = self.config.cron_clean_freq
         if self.base_dir is not None:
             job = self.my_cron.new(sys.executable +
-                                   " {0}/bin/clean_jobs.py > {0}/menage.log 2>&1".format(self.config.log_dir),
+                                   " {0}/bin/clean_jobs.py > {0}/clean.log 2>&1".format(self.config.log_dir),
                                    comment="dgenies")
-            job.day.every(menage_freq)
-            job.hour.on(menage_hour[0])
-            job.minute.on(menage_hour[1])
+            job.day.every(clean_freq)
+            job.hour.on(clean_time[0])
+            job.minute.on(clean_time[1])
             self.my_cron.write()
         else:
             raise Exception("Crons: base_dir must not be None")

src/dgenies/lib/job_manager.py

@@ -592,7 +592,7 @@ class JobManager:
                      "-n", self.query.get_name()]
         return self.launch_to_cluster(step="prepare",
                                       batch_system_type=batch_system_type,
-                                      command=self.config.cluster_python_script,
+                                      command=self.config.cluster_python_exec,
                                       args=args,
                                       log_out=self.logs,
                                       log_err=self.logs)

src/dgenies/views.py

@@ -175,7 +175,7 @@ def result(id_res):
 
 @app.route("/gallery", methods=['GET'])
 def gallery():
-    return render_template("gallery.html", items=Functions.get_gallery_items(), menu="gallery")
+    return render_template("gallery.html", items=Functions.get_gallery_items(), menu="gallery", title=app_title)
 
 
 @app.route("/gallery/<filename>", methods=['GET'])