Good version which works on DSL1

src/bioflowinsighterror.py

@@ -12,10 +12,10 @@ class BioFlowInsightError(Exception):
     def __init__(self, error, num=None, origin = None):
         self.origin = origin
         if(num!=None):
-            if(origin!=None):
-                super().__init__(f"[{num}] Error in the file '{self.origin.get_file_address()}': "+error)
-            else:
-                super().__init__(f"[{num}] {error}")
+            #if(origin!=None):
+            #    super().__init__(f"[{num}] Error in the file '{self.origin.get_file_address()}': "+error)
+            #else:
+            super().__init__(f"[{num}] {error}")
         else:
             super().__init__(f"{error}")
 

src/include.py

@@ -38,9 +38,6 @@ class Include(Nextflow_Building_Blocks):
     def get_duplicate_status(self):
         return self.nextflow_file_origin.get_duplicate_status()
 
-    def get_root_directory(self):
-        return self.origin.get_root_directory()
-
 
     #def get_list_name_includes(self):
     #    if(self.get_duplicate_status()):
@@ -67,7 +64,8 @@ class Include(Nextflow_Building_Blocks):
 
             if(address.split('/')[0] in ["$projectDir", "${projectDir}", "${baseDir}", "$baseDir"]):
                 address = '/'.join(address.split('/')[1:])
-                root = self.get_root_directory()
+                #root = self.get_root_directory()
+                root = self.nextflow_file_origin.get_root_directory()
             address = root+'/'+address
             if(os.path.isfile(address)):
                 found_file = True
@@ -79,14 +77,14 @@ class Include(Nextflow_Building_Blocks):
                 found_file = True
 
         if(not found_file and os.path.isfile(address[:-3]+"/main.nf")):
-            self.nextflow_file = Nextflow_File(address[:-3]+"/main.nf", workflow = self.nextflow_file_origin.get_workflow())
+            self.nextflow_file = Nextflow_File(address[:-3]+"/main.nf", workflow = self.nextflow_file_origin.get_workflow(), first_file=False)
         
         #TODO -> check if the nextflow_file is defined somewhere else? 
         #In the cas the nextflow file is imported multiple times
 
         else:
             if(os.path.isfile(address)):
-                self.nextflow_file = Nextflow_File(address, workflow = self.nextflow_file_origin.get_workflow())
+                self.nextflow_file = Nextflow_File(address, workflow = self.nextflow_file_origin.get_workflow(), first_file=False)
             else:
                 address = os.path.normpath(address)
                 raise BioFlowInsightError(f"Something went wrong in an include{self.get_string_line(self.get_code())}. No such file: '{address}'.", num = 10,origin=self)

src/main.py

@@ -85,38 +85,52 @@ class Main(Nextflow_Building_Blocks):
     
     def get_most_influential_conditions(self):
         most_influential_conditions = {}
-        all_calls = self.get_all_calls_in_subworkflow()
-        for c in all_calls:
-            if(c.get_first_element_called().get_type()=="Process"):
-                for condition in c.get_block().get_all_conditions(conditions = {}):
-                    try:
-                        temp = most_influential_conditions[condition]
-                    except:
-                        most_influential_conditions[condition] = 0
-                    most_influential_conditions[condition]+=1
-            if(c.get_first_element_called().get_type()=="Subworkflow"):
-                #Adding the number of calls from a process at the root of the subworkflow
-                num = 0
-                calls_at_root = c.get_first_element_called().root.get_calls_same_level()
-                for call_at_root in calls_at_root:
-                    for c_at_root in call_at_root.get_all_calls():
-                        if(c_at_root.get_first_element_called().get_type()=="Process"):
-                            num +=1
-                
-                most_influential_conditions_in_sub = c.get_first_element_called().get_most_influential_conditions()
-                #Adding the conditions from inside the subworkflow
-                for condition in most_influential_conditions_in_sub:
-                    try:
-                        temp = most_influential_conditions[condition]
-                    except:
-                        most_influential_conditions[condition] = 0
-                    num+=most_influential_conditions_in_sub[condition]
-                    most_influential_conditions[condition]+=most_influential_conditions_in_sub[condition]
-                #Adding calls from the subworkflow to the conditions
-                for condition in c.get_block().get_all_conditions(conditions = {}):
-                    try:
-                        temp = most_influential_conditions[condition]
-                    except:
-                        most_influential_conditions[condition] = 0
-                    most_influential_conditions[condition]+=num
-        return most_influential_conditions
+        if(self.nextflow_file.get_DSL()=="DSL2"):
+            all_calls = self.get_all_calls_in_subworkflow()
+            for c in all_calls:
+                if(c.get_first_element_called().get_type()=="Process"):
+                    for condition in c.get_block().get_all_conditions(conditions = {}):
+                        try:
+                            temp = most_influential_conditions[condition]
+                        except:
+                            most_influential_conditions[condition] = 0
+                        most_influential_conditions[condition]+=1
+                if(c.get_first_element_called().get_type()=="Subworkflow"):
+                    #Adding the number of calls from a process at the root of the subworkflow
+                    num = 0
+                    calls_at_root = c.get_first_element_called().root.get_calls_same_level()
+                    for call_at_root in calls_at_root:
+                        for c_at_root in call_at_root.get_all_calls():
+                            if(c_at_root.get_first_element_called().get_type()=="Process"):
+                                num +=1
+
+                    most_influential_conditions_in_sub = c.get_first_element_called().get_most_influential_conditions()
+                    #Adding the conditions from inside the subworkflow
+                    for condition in most_influential_conditions_in_sub:
+                        try:
+                            temp = most_influential_conditions[condition]
+                        except:
+                            most_influential_conditions[condition] = 0
+                        num+=most_influential_conditions_in_sub[condition]
+                        most_influential_conditions[condition]+=most_influential_conditions_in_sub[condition]
+                    #Adding calls from the subworkflow to the conditions
+                    for condition in c.get_block().get_all_conditions(conditions = {}):
+                        try:
+                            temp = most_influential_conditions[condition]
+                        except:
+                            most_influential_conditions[condition] = 0
+                        most_influential_conditions[condition]+=num
\ No newline at end of file
+            return most_influential_conditions
+        elif(self.nextflow_file.get_DSL()=="DSL1"):
+            processes = self.get_modules_defined()
+            for p in processes:
+                if(p.is_initialised()):
+                    for condition in p.origin.get_all_conditions(conditions = {}):
+                        try:
+                            temp = most_influential_conditions[condition]
+                        except:
+                            most_influential_conditions[condition] = 0
+                        most_influential_conditions[condition]+=1
+            return most_influential_conditions
+        else:
+            raise Exception("This shouldn't happen")
\ No newline at end of file

src/nextflow_building_blocks.py

@@ -83,8 +83,6 @@ class Nextflow_Building_Blocks:
     def get_name_file(self):
         return self.origin.get_name_file()
     
-    def get_root_directory(self):
-        return self.origin.get_root_directory()
     
     def get_rocrate_key(self, dico):
         return f"{self.get_file_address()[len(dico['temp_directory'])+1:]}#{self.get_name()}"

src/nextflow_file.py

@@ -40,6 +40,9 @@ class Nextflow_File(Nextflow_Building_Blocks):
     #GENERAL
     #----------------------
 
+    def get_root_directory(self):
+        return self.workflow.get_root_directory()
+
     def get_string_line(self, bit_of_code):
         return self.code.get_string_line(bit_of_code)
 

src/workflow.py

@@ -56,7 +56,7 @@ class Workflow:
                 with open(file, 'r') as f:
                     txt= f.read()
             else:
-                raise BioFlowInsightError("Multiple Nextflow files found at the root with no 'main.nf' file: I don't know which want to select")
+                raise BioFlowInsightError("Multiple Nextflow files found at the root with no 'main.nf' file: I don't know which one to select")
 
 
         
@@ -90,6 +90,10 @@ class Workflow:
         with open(self.output_dir / "debug" / "operations_in_call.nf",'w') as file:
             pass
 
+    def get_root_directory(self):
+        first_file = self.get_first_file()
+        return '/'.join(str(first_file.get_file_address()).split('/')[:-1])+"/"
+
     def get_conditions_2_ignore(self):
         return self.conditions_2_ignore