Merge branch 'genobioinfo' into 'master'

allow to create symlinks on genobioinfo

See merge request !148

workflows/download_symlink/__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/>.
 #
@@ -24,15 +24,17 @@ class DownloadSymlink (DownloadWorkflow):
     def get_description(self):
         return """This workflow allows you to create symbolic links of the selected data for the provided user in the destination directory on the server.
         Please be carefull that the provided user must have write permission on the specified directory on the server."""
-    
+
     def define_parameters(self, function="process"):
         config = NG6ConfigReader()
+        self.add_parameter("server",
+                   "Server where to create symbolic links",
+                   choices = ["genologin.toulouse.inra.fr","genobioinfo.toulouse.inrae.fr"],
+                   default="genologin")
         self.add_parameter('username', 'A valid user username on the server', type = "localuser" ,required = True)
         self.add_parameter('password', 'The connection password for the username on the server', type="password", required = True)
-        self.add_parameter('user_directory', """The directory where the links will be created. This directory must exists on the server and the 
-        provided user must have write permission on this directory""", default = config.get_user_base_directory(), 
-                           required = True, type="localdirectory")
-        
+        self.add_parameter('user_directory', 'The directory where the links will be created. This directory must exists on the server and the provided user must have write permission on this directory', default = config.get_user_base_directory(),
+                           required = True)
+
     def process(self):
-        self.add_component('CreateSymlink', [self.username, self.password, self.user_directory, self.data_id, self.run_id, self.analysis_id, self.admin_login])
-        
+        self.add_component('CreateSymlink', [self.username, self.password, self.user_directory, self.server, self.data_id, self.run_id, self.analysis_id, self.admin_login])
\ No newline at end of file

workflows/download_symlink/components/createsymlink.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/>.
 #
@@ -24,23 +24,24 @@ from ng6.utils import Utils
 
 from weaver.function import PythonFunction
 
-def create_symbolik_link (ids_dump_path, output_list, user_script, username, password, output_folder, ng6_username = None):
+def create_symbolik_link (ids_dump_path, output_list, user_script, username, password,server, output_folder, ng6_username = None):
     import os
     import pickle
     import subprocess
     import logging
-    
-    from ng6.config_reader import NG6ConfigReader 
+
+    from ng6.config_reader import NG6ConfigReader
     from ng6.utils import Utils, SSH
     from jflow.parameter import PasswordParameter
-    
+    logging.getLogger("create_symbolik_link").debug("Entering create_symbolik_link")
     config = NG6ConfigReader()
     data_folder = config.get_save_directory()
     password = PasswordParameter.decrypt(password)
     if ng6_username in ['', 'None', 'none', 'null', None] :
         ng6_username = None
-        
+
     try:
+
         fh = open(ids_dump_path, "rb")
         prefixed_ids = pickle.load(fh)
         fh.close()
@@ -48,13 +49,13 @@ def create_symbolik_link (ids_dump_path, output_list, user_script, username, pas
         src_directories, dest_directories = Utils.get_directories_structure_and_content(ng6_username, data_folder, output_folder, prefixed_ids)
         destinations = []
         with open(user_script, "w") as us:
-            
+
             with open(output_list, "w") as ol :
                 for i, source_dir in enumerate(src_directories):
                     dest_dir = dest_directories[i]
                     if not os.path.isdir(dest_dir) :
                         us.write("mkdir -p -m 755 %s ; \n"%dest_dir)
-                    
+
                     for filename in os.listdir(source_dir):
                         source_file_path = os.path.join(source_dir, filename)
                         dest_file_path = os.path.join(dest_dir, filename)
@@ -63,41 +64,50 @@ def create_symbolik_link (ids_dump_path, output_list, user_script, username, pas
                             if not os.path.exists(dest_file_path):
                                 us.write("ln -s %s %s ;\n"%(source_file_path,dest_file_path))
                             ol.write(dest_file_path+"\n")
-        
+
         # execution of the script as the user
         server_params = config.get_server_parameters()
-        s = SSH(username, password, server_params[0])
+        #s = SSH(username, password, server_params[0])
+        logging.getLogger("create_symbolik_link").debug("Before SSH(username, password, server) on server" + server)
+        logging.getLogger("create_symbolik_link").debug("user_script = "+user_script)
+        s = SSH(username, password, server)
+        logging.getLogger("create_symbolik_link").debug("Before s.cmd(")
+        logging.getLogger("create_symbolik_link").debug("user_script = "+user_script)
+        if server == "genobioinfo.toulouse.inrae.fr" :
+            user_script = user_script.replace("/home/ng6/work/", "/oldwork/ng6/")
+            user_script = user_script.replace("/work/ng6/", "/oldwork/ng6/")
+            logging.getLogger("create_symbolik_link").debug("user_script = "+user_script)
         s.cmd('bash %s'%user_script)
-        
+        logging.getLogger("create_symbolik_link").debug("After s.cmd(")
+
     except Exception as e:
         raise Exception('Unable to create link : %s'%e)
-    
+
 
 class CreateSymlink (Component):
-    
-    def define_parameters(self, username, password, user_directory, data_ids = [], run_ids = [], analysis_ids = [], login = None):
+
+    def define_parameters(self, username, password, user_directory, server, data_ids = [], run_ids = [], analysis_ids = [], login = None):
         self.add_parameter('login', 'The login of the user in ng6', type = 'ng6userlogin', default = login)
         self.add_parameter('username', 'Valid username on the server', required = True, default = username)
+        self.add_parameter('server', 'Server where to create smlinks', required = True, default = server)
         self.add_parameter('password', 'A password for the usernmae on the server', required = True, default = password, type = "password")
-        self.add_parameter('user_directory', 'Destination', required = True, default = user_directory)
+        self.add_parameter('user_directory', 'Destination', required = False, default = user_directory)
         self.add_parameter_list('data_ids', 'Ids or a run from which rawdata will be retrieved', default = data_ids)
         self.add_parameter_list('run_ids', 'Ids of run from which all data will be retrieved', default = run_ids)
         self.add_parameter_list('analysis_ids', 'Ids of analysis to retrieve', default = analysis_ids)
         self.add_output_file( 'user_script', 'The bash script that will be executed by the user', filename = "userscript.sh")
         self.add_output_file( 'output_list', 'output_list', filename = "output_list.txt")
-        
+
     def process(self):
         run_ids = [ "run_%s"%i for i in self.run_ids ]
         data_ids = [ "data_%s"%i for i in self.data_ids ]
         analysis_ids = [ "analyse_%s"%i for i in self.analysis_ids ]
-        
+
         ids_dump_path = self.get_temporary_file(".dump")
         fh = open(ids_dump_path, "wb")
         pickle.dump( run_ids + data_ids + analysis_ids, fh)
         fh.close()
-        
+
         createlinks = PythonFunction(create_symbolik_link, cmd_format = "{EXE} {IN} {OUT} {ARG} ")
-        createlinks(arguments = [ self.username, self.password, self.user_directory, self.login ], 
-                    inputs = ids_dump_path , outputs = [self.output_list, self.user_script], local = True)
-        
-        
\ No newline at end of file
+        createlinks(arguments = [ self.username, self.password, self.server, self.user_directory, self.login ],
+                    inputs = ids_dump_path , outputs = [self.output_list, self.user_script], local = True)
\ No newline at end of file