#89 : rundate and analysis date are set one day before the real date

src/ng6/t3MySQLdb.py

@@ -22,7 +22,7 @@ __version__ = '1.0'
 __email__ = 'support.bioinfo.genotoul@inra.fr'
 __status__ = 'beta'
 
-import datetime, time, logging
+import datetime, time, calendar, logging
 import pymysql
 import pymysql.cursors
 import collections
@@ -183,7 +183,7 @@ class t3MySQLdb(object):
         if self.project_exists(name) :
             raise ValueError("Impossible to create project %s, this name is already used!"%name)
         
-        crdate = str(time.mktime(datetime.date.today().timetuple())).split(".")[0]
+        crdate = str(time.time()).split(".")[0]
         if cruser_login: # If the administrator login is specified
             admin_id = self.get_user_id(cruser_login)
             
@@ -298,13 +298,14 @@ class t3MySQLdb(object):
           @param cruser_login  : the create user login
           @param hidden        : is the analysis hidden
         """
+        logging.getLogger("t3MySQLdb.add_run").debug("Inserting run with date of run =" + str(date))
         cruser_id = self.get_user_id(cruser_login)
-        crdate = str(time.mktime(datetime.date.today().timetuple())).split(".")[0]
+        crdate = str(time.time()).split(".")[0]
         retention_date = time.mktime((datetime.date.today() + datetime.timedelta(days=365*int(self.cfg_reader.get_retention_time()))).timetuple())
         sql = "INSERT INTO tx_nG6_run (pid, tstamp, crdate, cruser_id, name, date, directory, species, data_nature,\
         type, nb_sequences, full_seq_size, description, hidden, sequencer, retention_date, data_state, purged_date, purged_size, mail_sent_date) VALUES ('%s', '%s', '%s', %s, '%s', '%s','%s',\
         '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s')" % ( self.cfg_reader.get_pid(), crdate, crdate, cruser_id, self.esc_q(name), 
-                                                             time.mktime(date.timetuple()), directory, self.esc_q(species), 
+                                                             calendar.timegm(date.timetuple()), directory, self.esc_q(species), 
                                                              self.esc_q(data_nature), self.esc_q(type), nb_sequences, 
                                                              full_seq_size, self.esc_q(description), hidden, self.esc_q(sequencer),retention_date, "stored","0","0","0")
         qresult = self.execute(sql, commit = True)
@@ -324,7 +325,7 @@ class t3MySQLdb(object):
           @param project_id    : the project_id the run belong to
           @param run_id        : the run to add
         """
-        crdate = str(time.mktime(datetime.date.today().timetuple())).split(".")[0]
+        crdate = str(time.time()).split(".")[0]
         sql = "INSERT INTO tx_nG6_project_run (pid, tstamp, crdate, project_id, run_id) \
         VALUES('%s', '%s', '%s', '%s','%s')" % ( self.cfg_reader.get_pid(), crdate, crdate, project_id, run_id)
         self.execute(sql, commit = True)
@@ -581,7 +582,7 @@ class t3MySQLdb(object):
           @param name        : the sample name
           @return sample id
         """
-        crdate = str(time.mktime(datetime.date.today().timetuple())).split(".")[0]
+        crdate = str(time.time()).split(".")[0]
         column_names = [ 'pid', 'tstamp', 'run_id', 'sample_id', 'reads1' ]
         column_vals = [ "'%s'" % self.cfg_reader.get_pid(), 
                        "'%s'" % crdate, 
@@ -676,7 +677,7 @@ class t3MySQLdb(object):
           @param is_editable : True if analysis has been added by an user
         """
         cruser_id = self.get_user_id(cruser_login)
-        crdate = str(time.mktime(datetime.date.today().timetuple())).split(".")[0]
+        crdate = str(time.time()).split(".")[0]
         retention_date = time.mktime((datetime.date.today() + datetime.timedelta(days=365*int(self.cfg_reader.get_retention_time()))).timetuple())
         
         if is_editable : analysis_is_editable = 1 
@@ -707,7 +708,7 @@ class t3MySQLdb(object):
           @param project_id  : the project_id the analysis has been done on
           @param analysis_id  : the analysis id
         """
-        crdate = str(time.mktime(datetime.date.today().timetuple())).split(".")[0]
+        crdate = str(time.time()).split(".")[0]
         sql = "INSERT INTO tx_nG6_project_analyze (pid, tstamp, crdate, project_id,\
          analyze_id) VALUES('%s','%s','%s','%s','%s')" % ( self.cfg_reader.get_pid(), crdate, crdate, project_id, analysis_id ) 
         self.execute(sql, commit = True)
@@ -718,7 +719,7 @@ class t3MySQLdb(object):
           @param run_id      : the run_id the analysis has been done on
           @param analysis_id  : the analysis id
         """
-        crdate = str(time.mktime(datetime.date.today().timetuple())).split(".")[0]
+        crdate = str(time.time()).split(".")[0]
         sql = "INSERT INTO tx_nG6_run_analyze (pid, tstamp, crdate, run_id, analyze_id) \
         VALUES('%s', '%s', '%s', '%s', '%s')" % ( self.cfg_reader.get_pid(), crdate, crdate, run_id, analysis_id) 
         self.execute(sql, commit = True )
@@ -732,7 +733,7 @@ class t3MySQLdb(object):
           @param value      : the result value
           @param group      : the group value
         """
-        crdate = str(time.mktime(datetime.date.today().timetuple())).split(".")[0]
+        crdate = str(time.time()).split(".")[0]
         sql = "INSERT INTO tx_nG6_result (pid, tstamp, crdate, analyze_id, file, rkey, rvalue, rgroup) \
         VALUES('%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s')" % ( self.cfg_reader.get_pid(), crdate, crdate, 
                                                                     analysis_id, file, key, value, group )
@@ -993,7 +994,7 @@ class t3MySQLdb(object):
         return(qresult)
                 
     def set_purge_demand_deleted(self, demand_ids):
-        date = str(time.mktime(datetime.date.today().timetuple())).split(".")[0]
+        date = str(time.time()).split(".")[0]
         parts = [
                     'SELECT',
                         'tx_nG6_purge_demand.uid AS demand_id,',