New "switch_projet_space_id" workflow, update for t3MySQLdb.py.

The new workflow allows to migrate a project to a space_id defined in
application.properties.
Every run and analyse gets a new retention and new path, the directories
and files are moved, the old directories are removed.

Use:
python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py
switchprojectspaceid --project-id 1292 --space-id default --admin-login
CTD

issue #129

src/ng6/t3MySQLdb.py

@@ -1031,3 +1031,64 @@ class t3MySQLdb(object):
                 self.update_fields('tx_nG6_purge_demand',demand_ids,
                         ["processed_date","demand_state"],
                         [date,"deleted"])
+    
+    def set_run_retention_from_duration(self, run_id, duration):
+        """
+        Updates a run's retention from a given duration (in months)
+          @param run_id      : the run id
+          @param duration    : the duration (in months)
+        """
+        sql = "UPDATE tx_nG6_run SET retention_date = UNIX_TIMESTAMP(TIMESTAMPADD(MONTH,%s,FROM_UNIXTIME(crdate))) WHERE uid= '%s' "% ( duration, run_id )
+        self.execute(sql, commit = True )
+        
+    def set_analysis_retention_from_duration(self, analysis_id, duration):
+        """
+        Updates a run's retention from a given duration (in months)
+          @param analysis_id : the analysis id
+          @param duration    : the duration (in months)
+        """
+        sql = "UPDATE tx_nG6_analyze SET retention_date = UNIX_TIMESTAMP(TIMESTAMPADD(MONTH,%s,FROM_UNIXTIME(crdate))) WHERE uid= '%s' "% ( duration, analysis_id )
+        self.execute(sql, commit = True )
+        
+    def set_run_retention_from_date(self, run_id, date):
+        """
+        Updates a run's retention from a given date 
+          @param run_id      : the run id
+          @param date        : the date (format dd/mm/yyyy)
+        """
+        sql = "UPDATE tx_nG6_run SET retention_date = UNIX_TIMESTAMP( str_to_date('%s','%d/%m/%Y')) WHERE uid= '%s' "% ( date, run_id )
+        self.execute(sql, commit = True )
+        
+    def set_analysis_retention_from_date(self, analysis_id, date):
+        """
+        Updates a run's retention from a given date
+          @param analysis_id : the analysis id
+          @param date        : the date (format dd/mm/yyyy)
+        """
+        sql = "UPDATE tx_nG6_analyze SET retention_date = UNIX_TIMESTAMP( str_to_date('%s','%d/%m/%Y')) WHERE uid= '%s' "% ( date, analysis_id )
+        self.execute(sql, commit = True )
+    
+    def set_run_retention_from_epoch_timestamp(self, run_id, date):
+        """
+        Updates a run's retention from a given duration (in months)
+          @param run_id      : the run id
+          @param duration    : the duration (in months)
+        """
+        sql = "UPDATE tx_nG6_run SET retention_date = '%s' WHERE uid= '%s' "% ( date, run_id )
+        self.execute(sql, commit = True )
+    
+    def set_analysis_retention_from_depoch_timestamp(self, analysis_id, duration):
+        """
+        Updates a run's retention from a given duration (in months)
+          @param analysis_id : the analysis id
+          @param duration    : the duration (in months)
+        """
+        sql = "UPDATE tx_nG6_analyze SET retention_date = '%s' WHERE uid= '%s' "% ( duration, analysis_id )
+        self.execute(sql, commit = True )
+        
+    def get_run_analyzes_id_from_project(self, project_id):
+        sql = "SELECT analyze_id FROM tx_nG6_view_project_run_analyze WHERE project_id='%s'"  % project_id
+        qresult = self.execute(sql)
+        return [ r[0] for r in qresult.rows ]    
+        
+        
\ No newline at end of file

workflows/switch_project_space_id/__init__.py

+#
+# Copyright (C) 2015 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import os
+import sys
+import logging
+import shutil
+
+from ng6.ng6workflow import BasicNG6Workflow
+from ng6.config_reader import NG6ConfigReader
+from ng6.utils import Utils
+
+from ng6.project import Project
+from ng6.run import Run
+from ng6.analysis import Analysis
+
+from ng6.t3MySQLdb import t3MySQLdb
+
+class SwitchProjectSpaceId (BasicNG6Workflow):
+
+    def get_description(self):
+        return """This workflow allows you to migrate a project from a space_id to another.  
+        It updates the project's space_id in DB, moves the runs files, updates the runs and analyzes's files paths, and updates the corresponding retentions."""
+    
+    def define_parameters(self, function="process"):
+        self.add_parameter('project_id', 'The project id', type=int, required = True)
+        self.add_parameter('space_id', 'The new space_id', required = True)
+        
+    def process(self):
+        
+        #self.space_id = self.space_id
+        #self.project_id = self.project_id
+        self.project_id = int(self.project_id)
+        
+        if self.project_id and self.space_id :
+            self.project = Project.get_from_id(self.project_id)
+            old_space_id = self.project.space_id
+            
+            #Update to the projcet's space_id
+            t3mysql = t3MySQLdb()
+            t3mysql.update_fields('tx_nG6_project', str(self.project_id), ['space_id'], [str(self.space_id)] )
+            
+            #Retrieve the old and new directories
+            ng6conf = NG6ConfigReader()
+            old_directory = ng6conf.get_space_directory(old_space_id)
+            new_directory = ng6conf.get_space_directory(self.space_id)
+            
+            new_retention = ng6conf.get_retention_date(self.space_id)
+            base_path = ng6conf.get_save_directory()
+            
+            #Process for the project's runs
+            runs_ids = t3mysql.get_project_runs_ids(self.project_id)
+            for run_id in runs_ids :
+                path_old_run_directory = base_path + t3mysql.select_run_directory(run_id)
+                path_new_run_directory = path_old_run_directory.replace(old_directory,new_directory)
+                
+                #Update the directory in DB
+                new_run_directory = t3mysql.select_run_directory(run_id)
+                new_run_directory = new_run_directory.replace(old_directory, new_directory)
+                t3mysql.update_fields('tx_nG6_run', str(run_id), ['directory'], [str(new_run_directory)] )
+                
+                #Moving the files
+                if not os.path.isdir(path_new_run_directory) :
+                    os.mkdir(path_new_run_directory)   
+                
+                try:
+                    shutil.move(path_old_run_directory, path_new_run_directory)
+                except Exception as err:
+                    logging.getLogger("SwitchProjectSpaceId.process").error("Error while moving " + path_old_run_directory + " to " + path_new_run_directory + " \n" + str(err))
+                    raise Exception("Error while moving " + path_old_run_directory + " to " + path_new_run_directory + " \n" + str(err))
+                
+                #Delete the old directory if empty
+                if os.path.isdir(path_old_run_directory) and not os.listdir(path_old_run_directory) :
+                    os.rmdir(path_old_run_directory)
+                
+                #Update the retention in DB
+                t3mysql.set_run_retention_from_epoch_timestamp(run_id, new_retention)
+                
+            #Process for the project's analyzes
+            analyzes_ids = t3mysql.get_project_analysis_ids(self.project_id)
+            for analysis_id in analyzes_ids :
+                path_old_analysis_directory = base_path + t3mysql.select_analysis_directory(analysis_id)
+                path_new_analysis_directory = path_old_analysis_directory.replace(old_directory,new_directory)
+                
+                #Update the directory in DB
+                new_analysis_directory = t3mysql.select_analysis_directory(analysis_id)
+                new_analysis_directory = new_analysis_directory.replace(old_directory, new_directory)
+                t3mysql.update_fields('tx_nG6_analyze', str(analysis_id), ['directory'], [str(new_analysis_directory)] )
+                
+                #Moving the files
+                if not os.path.isdir(path_new_run_directory) :
+                    os.mkdir(path_new_analysis_directory) 
+                
+                try:
+                    shutil.move(path_old_analysis_directory, path_new_analysis_directory)
+                except Exception as err:
+                    logging.getLogger("SwitchProjectSpaceId.process").error("Error while moving " + path_old_analysis_directory + " to " + path_new_analysis_directory + " \n" + str(err))
+                    raise Exception("Error while moving " + path_old_analysis_directory + " to " + path_new_analysis_directory + " \n" + str(err))
+                
+                #Delete the old directory if empty
+                if os.path.isdir(path_old_analysis_directory) and not os.listdir(path_old_analysis_directory) :
+                    os.rmdir(path_old_analysis_directory)
+                
+                #Update the retention in DB
+                t3mysql.set_analysis_retention_from_depoch_timestamp(analysis_id, new_retention)
+                
+            #Process for the project's run's analyzes
+            run_analyzes_ids = t3mysql.get_run_analyzes_id_from_project(self.project_id)
+            for analysis_id in run_analyzes_ids :
+                path_old_analysis_directory = base_path + t3mysql.select_analysis_directory(analysis_id)
+                path_new_analysis_directory = path_old_analysis_directory.replace(old_directory,new_directory)
+                
+                #Update the directory in DB
+                new_analysis_directory = t3mysql.select_analysis_directory(analysis_id)
+                new_analysis_directory = new_analysis_directory.replace(old_directory, new_directory)
+                t3mysql.update_fields('tx_nG6_analyze', str(analysis_id), ['directory'], [str(new_analysis_directory)] )
+                
+                #Moving the files
+                if not os.path.isdir(path_new_analysis_directory) :
+                    os.mkdir(path_new_analysis_directory) 
+                
+                try:
+                    shutil.move(path_old_analysis_directory, path_new_analysis_directory)
+                except Exception as err:
+                    logging.getLogger("SwitchProjectSpaceId.process").error("Error while moving " + path_old_analysis_directory + " to " + path_new_analysis_directory + " \n" + str(err))
+                    raise Exception("Error while moving " + path_old_analysis_directory + " to " + path_new_analysis_directory + " \n" + str(err))
+                
+                #Delete the old directory if empty
+                if os.path.isdir(path_old_analysis_directory) and not os.listdir(path_old_analysis_directory) :
+                    os.rmdir(path_old_analysis_directory)
+                
+                #Update the retention in DB
+                t3mysql.set_analysis_retention_from_depoch_timestamp(analysis_id, new_retention)
\ No newline at end of file

workflows/switch_project_space_id/components/__init__.py

+#
+# Copyright (C) 2015 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
\ No newline at end of file