Split the current NG6Workflow into two class

- One will handle a workflow without run (BasicNG6Workflow)
- the other will handle runs ( NG6Workflow)

src/ng6/ng6workflow.py

@@ -33,40 +33,25 @@ from ng6.run import Run
 def adminlogin(login):
     t3mysql = t3MySQLdb()
     try:
-	t3mysql.get_user_id(login)
+        t3mysql.get_user_id(login)
         return login
     except:
         raise argparse.ArgumentTypeError("Login '" + login + "' does not exists! Please provide a valid login!")
 
-class NG6Workflow (Workflow):
-    """
-    """             
 
-    def __init__(self, args={}, id=None, function= "process", parameters_section="parameters", add_run_params=True):
+class BasicNG6Workflow (Workflow):
+
+    def __init__(self, args={}, id=None, function= "process", parameters_section="parameters"):
         Workflow.__init__(self, args, id, function, parameters_section)
+        self._required_parameters = [Parameter("admin_login", "Who is the project administrator", "--admin-login", required=True, type=adminlogin, display_name="Admin login")]
         # admin login is required for all workflow
-        self.add_run_params = add_run_params
-        self.parameters.extend(self._add_required_parameters())
+        self.parameters.extend(self._required_parameters)
         self.args = self._extend_and_format_args(self.parameters, args)
 
-    def _add_required_parameters(self):
-        orequired = []
-        orequired.append(Parameter("admin_login", "Who is the project administrator", "--admin-login", required=True, type=adminlogin, display_name="Admin login"))
-        # add run parameters
-        if self.add_run_params: 
-            orequired.append(Parameter("project_id", "The project id the run belongs to", "--project-id", required=True, type=int, group="Run information"))
-            orequired.append(Parameter("run_name", "Give a name to your run", "--name", required=True, group="Run information", display_name="Name"))
-            orequired.append(Parameter("run_description", "Give a description to your run", "--description", required=True, group="Run information", display_name="Description"))
-            orequired.append(Parameter("run_date", "When were the data produced","--date",  required=True, type=date, group="Run information", display_name="Date"))
-            orequired.append(Parameter("data_nature", "Are Sequences cDNA, genomique, RNA, ...", "--data-nature", required=True, group="Run information", display_name="Data nature"))
-            orequired.append(Parameter("sequencer", "Which sequencer produced the data", "--sequencer", required=True, group="Run information", display_name="Sequencer"))
-            orequired.append(Parameter("species", "Which species has been sequenced", "--species", required=True, group="Run information", display_name="Species"))
-            orequired.append(Parameter("run_type", "What type of data is it (1 lane, 1 region)", "--type", required=True, group="Run information", display_name="Type"))        
-        return orequired
 
     def get_parameters_per_groups(self, parameters_section="parameters"):
         name, description, parameters = self._get_from_config(parameters_section)
-        parameters.extend(self._add_required_parameters())
+        parameters.extend(self._required_parameters)
         pgparameters, parameters_order = {}, []
         for param in parameters:
             if param.group not in parameters_order: parameters_order.append(param.group)
@@ -75,53 +60,8 @@ class NG6Workflow (Workflow):
             else:
                 pgparameters[param.group] = [param]
         return [pgparameters, parameters_order]
-
-    def pre_process(self):
-
-        self.project = None
-        self.runobj = None
-        # if starting from an existing project
-        if self.args.has_key("project_id") and self.args["project_id"] is not None:
-            self.project = Project.get_from_id(self.args["project_id"])
-            self.metadata.append("project_id="+str(self.args["project_id"]))
-            # if user is not allowed to add data on project (is not admin)
-            if self.project is not None and not self.project.is_admin(self.args["admin_login"]):
-                sys.stderr.write( "The user login '" + self.args["admin_login"] + "' is not allowed to add data on project '" + self.project.name + "'.\n" )
-                sys.exit()
-        # if starting from a brand new project
-        elif self.args.has_key("project_name") and self.args.has_key("project_description") and self.args.has_key("admin_login"):
-            self.project = Project(self.args["project_name"], self.args["project_description"], self.args["admin_login"])
-            self.metadata.append("project_id="+str(self.project.id))
-
-        # if starting from an existing run
-        if self.args.has_key("run_id") and self.args["run_id"] is not None:
-            if self.project is None :
-                project = Project.get_from_run_id(self.args["run_id"])
-                # if user is not allowed to add data on project (is not admin)
-                if not project.is_admin(self.args["admin_login"]):
-                    sys.stderr.write( "The user login '" + self.args["admin_login"] + "' is not allowed to add data on project '" + project.name + "'." )
-                    sys.exit()
-            self.runobj = Run.get_from_id(self.args["run_id"])
-            self.metadata.append("run_id="+str(self.args["run_id"]))
-        # if starting from a brand new run
-        elif self.args.has_key("run_date") and self.args.has_key("run_name") and self.args.has_key("species") and self.args.has_key("data_nature") \
-            and self.args.has_key("run_type") and self.args.has_key("run_description") and self.args.has_key("sequencer") and self.args.has_key("project_id"):
-            # build the run
-            self.runobj = Run(self.args["run_name"], self.args["run_date"], self.args["species"], self.args["data_nature"], 
-                              self.args["run_type"], self.args["run_description"], self.args["sequencer"])
-            self.runobj.admin_login=self.args["admin_login"]
-            # then add the run to the project
-            self.project.add_run(self.runobj)
-            # if it's a run with some index, let's write down description
-            if self.args.has_key("sample") and self.args["sample"]:
-                try:
-                    samples = {}
-                    for sample in self.args["sample"]:
-                        samples[sample["sample_name"]] = sample["sample_description"]
-                    self.runobj.add_mids_description(samples)
-                except: pass
-            self.metadata.append("run_id="+str(self.runobj.id))
     
+
     def add_component(self, component_name, args=[], kwargs={}, component_prefix="default", parent=None, addto="run"):
         # first build and check if this component is OK
         if self.comp_pckg.has_key(component_name):
@@ -176,6 +116,55 @@ class NG6Workflow (Workflow):
             return cmpt_object
         else:
             raise ImportError(component_name + " component cannot be loaded, available components are: {0}".format(", ".join(self.comp_pckg.keys())))
+
+
+class NG6Workflow (BasicNG6Workflow):
+
+    def __init__(self, args={}, id=None, function= "process", parameters_section="parameters"):
+        BasicNG6Workflow.__init__(self, args, id, function, parameters_section)
+        self._required_parameters.extend(self._add_required_parameters())
+        self.parameters.extend(self._required_parameters)
+        self.args = self._extend_and_format_args(self.parameters, args)
+
+    def _add_required_parameters(self):
+        orequired = []
+        orequired.append(Parameter("project_id", "The project id the run belongs to", "--project-id", required=True, type=int, group="Run information"))
+        orequired.append(Parameter("run_name", "Give a name to your run", "--name", required=True, group="Run information", display_name="Name"))
+        orequired.append(Parameter("run_description", "Give a description to your run", "--description", required=True, group="Run information", display_name="Description"))
+        orequired.append(Parameter("run_date", "When were the data produced","--date",  required=True, type=date, group="Run information", display_name="Date"))
+        orequired.append(Parameter("data_nature", "Are Sequences cDNA, genomique, RNA, ...", "--data-nature", required=True, group="Run information", display_name="Data nature"))
+        orequired.append(Parameter("sequencer", "Which sequencer produced the data", "--sequencer", required=True, group="Run information", display_name="Sequencer"))
+        orequired.append(Parameter("species", "Which species has been sequenced", "--species", required=True, group="Run information", display_name="Species"))
+        orequired.append(Parameter("run_type", "What type of data is it (1 lane, 1 region)", "--type", required=True, group="Run information", display_name="Type"))        
+        return orequired
+
+    def pre_process(self):
+        self.project = None
+        self.runobj = None
+        
+        # start from an existing project
+        self.project = Project.get_from_id(self.args["project_id"])
+        self.metadata.append("project_id="+str(self.args["project_id"]))
+        # if user is not allowed to add data on project (is not admin)
+        if self.project is not None and not self.project.is_admin(self.args["admin_login"]):
+            sys.stderr.write( "The user login '" + self.args["admin_login"] + "' is not allowed to add data on project '" + self.project.name + "'.\n" )
+            sys.exit()
+
+        # build the run
+        self.runobj = Run(self.args["run_name"], self.args["run_date"], self.args["species"], self.args["data_nature"], 
+                          self.args["run_type"], self.args["run_description"], self.args["sequencer"])
+        self.runobj.admin_login=self.args["admin_login"]
+        # then add the run to the project
+        self.project.add_run(self.runobj)
+        # if it's a run with some index, let's write down description
+        if self.args.has_key("sample") and self.args["sample"]:
+            try:
+                samples = {}
+                for sample in self.args["sample"]:
+                    samples[sample["sample_name"]] = sample["sample_description"]
+                self.runobj.add_mids_description(samples)
+            except: pass
+        self.metadata.append("run_id="+str(self.runobj.id))
         
     def post_process(self):
         # once everything done, sync directories
@@ -183,4 +172,3 @@ class NG6Workflow (Workflow):
             self.runobj.sync()
         elif self.project:
             self.project.sync()
-            

workflows/addanalysis/__init__.py

@@ -18,13 +18,11 @@
 import os
 import sys
 
-from ng6.ng6workflow import NG6Workflow
+from ng6.ng6workflow import BasicNG6Workflow
+from ng6.project import Project
+from ng6.run import Run
 
-
-class AddAnalysis (NG6Workflow):
-    
-    def __init__(self, args={}, id=None, function= "process", parameters_section="parameters"):
-        NG6Workflow.__init__(self, args, id, function, parameters_section, add_run_params=False)
+class AddAnalysis (BasicNG6Workflow):
     
     def process(self):
         """ 
@@ -37,16 +35,24 @@ class AddAnalysis (NG6Workflow):
                 files_to_save.append(file)
             else:
                 sys.exit("error: %s file does not exists\n" % (file))
-        # Check if user provided a project or a run
-        if self.project and self.runobj:
-            sys.stderr.write("An analysis should be added to a run OR a project not both of them!\n")
-            sys.exit()
-        elif self.project is None and self.runobj is None :
+
+        # Check if user provided a project or a run        
+        if self.args["project_id"] :
+            self.project = Project.get_from_id(self.args["project_id"])
+            self.metadata.append("project_id="+str(self.args["project_id"]))
+            # if user is not allowed to add data on project (is not admin)
+            if self.project is not None and not self.project.is_admin(self.args["admin_login"]):
+                sys.stderr.write( "The user login '" + self.args["admin_login"] + "' is not allowed to add data on project '" + self.project.name + "'.\n" )
+                sys.exit()
+        elif self.args["run_id"] :
+            self.runobj = Run.get_from_id(self.args["run_id"])
+            self.metadata.append("run_id="+str(self.args["run_id"]))
+        else :
             sys.stderr.write("One of run_id or project_id parameter is required!\n")
             sys.exit()
+        
+        addto = "project" if self.project else "run"
 
-        addto = "run"
-        if self.project: addto = "project"
         basicanalysis = self.add_component("BasicAnalyse", [files_to_save, self.args["analysis_name"], 
                         self.args["analysis_description"], self.args["analysis_software"], self.args["analysis_software_options"], 
                         self.args["analysis_software_version"], self.args["compression"], self.args["delete"], 

workflows/addanalysis/workflow.properties

@@ -61,11 +61,13 @@ project_id.name = project_id
 project_id.flag = --project-id
 project_id.help = The project id the analysis belongs to
 project_id.type = int
+project_id.exclude = run_id
 
 run_id.name = run_id
 run_id.flag = --run-id
 run_id.help = The run id the run belongs to
 run_id.type = int
+run_id.exclude = project_id
 
 analysis_name.name = analysis_name
 analysis_name.flag = --analysis-name

workflows/addproject/__init__.py

@@ -15,16 +15,14 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-from ng6.ng6workflow import NG6Workflow
+from ng6.ng6workflow import BasicNG6Workflow
+from ng6.project import Project
 
-
-class AddProject (NG6Workflow):
-
-    def __init__(self, args={}, id=None, function= "process", parameters_section="parameters"):
-        NG6Workflow.__init__(self, args, id, function, parameters_section, add_run_params=False)
+class AddProject (BasicNG6Workflow):
 
     def process(self):
         """ 
         Run the workflow
         """
-        pass
+        project = Project(self.args["project_name"], self.args["project_description"], self.args["admin_login"])
+        self.metadata.append("project_id="+str(project.id))