Update addanalysis workflow to link the basicanalysis to any existing analysis...

Update addanalysis workflow to link the basicanalysis to any existing analysis using the analysis id.
email type check.

src/ng6/analysis.py

@@ -45,7 +45,7 @@ from jflow.component import Component
 from weaver.function import PythonFunction
 
 
-def add_analysis(analysis_cfg, *input_files):
+def add_analysis(parent_id, analysis_cfg, *input_files):
     from ng6.analysis import Analysis
     from ng6.project import Project
     from ng6.run import Run
@@ -66,6 +66,9 @@ def add_analysis(analysis_cfg, *input_files):
         if os.path.isfile(parent_analysis_cfg):
             parent = Analysis.get_from_file(parent_analysis_cfg)
             analysis.parent = parent
+    elif parent_id != 'none' :
+        parent = Analysis.get_from_id(int(parent_id))
+        analysis.parent = parent
 
     # process the parsing of the analysis
     analysis.post_process()
@@ -166,6 +169,7 @@ class Analysis (Component):
         analysis_dump.close()
         inputs.append(analysis_dump_path)
         
+        parent_id = 'none'
         wait_for_files = []
         for attr in self.__dict__:
             # TODO if no Output object raise error
@@ -175,13 +179,16 @@ class Analysis (Component):
             elif self.__getattribute__(attr).__class__.__name__ == "OutputFileList":
                 wait_for_files.extend(self.__getattribute__(attr))
         if self.parent:
-            inputs.append(self.parent.get_config_file_path())
+            if self.parent.id:
+                parent_id = self.parent.id
+            else :
+                inputs.append(self.parent.get_config_file_path())
         # then run the component
         self.process()
         
         # add the add_analysis command lines to the make
-        add = PythonFunction(add_analysis, cmd_format="{EXE} {OUT} {IN}")
-        add(includes=wait_for_files, outputs=self.get_config_file_path(), inputs=inputs)
+        add = PythonFunction(add_analysis, cmd_format="{EXE} {ARG} {OUT} {IN}")
+        add(includes=wait_for_files, outputs=self.get_config_file_path(), inputs=inputs, arguments=parent_id)
     
     def __str__(self):
         """

workflows/addanalysis/__init__.py

@@ -21,6 +21,7 @@ import sys
 from ng6.ng6workflow import BasicNG6Workflow
 from ng6.project import Project
 from ng6.run import Run
+from ng6.analysis import Analysis
 
 class AddAnalysis (BasicNG6Workflow):
     
@@ -32,13 +33,14 @@ class AddAnalysis (BasicNG6Workflow):
         self.add_parameter("compression", "How should data be compressed once archived", choices = ['none', 'gz', 'bz2'], default = 'none')
         self.add_parameter("delete", "Should the input data be deleted once the process is over", type = bool , default = False)
         self.add_parameter("archive_name", "Give a name to the final archive", default = 'ng6_archive')
-        self.add_parameter("project_id", "The project id the analysis belongs to", type = int, required = True)
-        self.add_parameter("run_id", "The run id the run belongs to", type = int, required = True)
+        self.add_parameter("project_id", "The project id the analysis belongs to", type = 'int', required = True)
+        self.add_parameter("run_id", "The run id the run belongs to", type = 'int', required = True)
         self.add_parameter("analysis_name", "Give a name to your analysis", required = True)
         self.add_parameter("analysis_description", "Give a description to your analysis", required = True)
         self.add_parameter("analysis_software", "Which software was used for this analysis", required = True)
         self.add_parameter("analysis_software_options", "Which software options were used for this analysis", required = True)
         self.add_parameter("analysis_software_version", "analysis_software_version", required = True)
+        self.add_parameter("parent_analysis", "The id of an analysis to be used as a parent analysis", type= 'int')
         self.add_exclusion_rule( "project_id", "run_id" )
     
     def process(self):
@@ -68,11 +70,12 @@ class AddAnalysis (BasicNG6Workflow):
             sys.exit()
         
         addto = "project" if self.project else "run"
-
+        parent = Analysis.get_from_id(self.parent_analysis) if self.parent_analysis else None
+        
         basicanalysis = self.add_component("BasicAnalyse", [files_to_save, self.analysis_name, 
                         self.analysis_description, self.analysis_software, self.analysis_software_options, 
                         self.analysis_software_version, self.compression, self.delete, 
-                        self.archive_name], addto=addto)        
+                        self.archive_name], addto=addto, parent = parent)        
 
     def post_process(self):
         if self.runobj:

workflows/types.py

@@ -19,6 +19,7 @@ import argparse
 import datetime
 import os
 import pwd
+import re
 
 from ng6.t3MySQLdb import t3MySQLdb
 
@@ -101,6 +102,9 @@ def password(val):
     return val
 
 def email(val):
+    if not re.match( r'[^@]+@[^@]+\.[^@]+', val) :
+        raise argparse.ArgumentTypeError("Invalid email '%s' " % val)
+    
     return val
 
 def samplemetadata(metadata):