Fix minor bug

src/operation.py

@@ -84,35 +84,42 @@ class Operation(Executor):
     #I don't need to define the equivalent gives -> cause it's not possible:)
     def add_origin_emits(self, full_code, name_called, name_emitted):
         from .emitted import Emitted
-        #full_code, name_called, name_emitted = match.group(1), match.group(2), match.group(3)
-        IGNORE_NAMES = ['params']
-        #In the cas an operator is extracted at the end of the emit
-        if(full_code.count('.')>=2):
-            splited = full_code.split('.')
-            if( splited[-1] in constant.LIST_OPERATORS):
-                full_code = '.'.join(splited[:-1])
-        if(name_called not in IGNORE_NAMES):
-            process = self.origin.get_process_from_name(name_called)
-            subworkflow = self.origin.get_subworkflow_from_name(name_called)
-
-            if(process!=None and subworkflow!=None):
-                raise Exception(f"Problem in get_element -> {name_called} exists as process and subworkflow")
-            #Case subworkflow
-            if(process==None and subworkflow!=None):
-                emitted = Emitted(name=full_code, origin=self.origin, emitted_by=subworkflow)
-                emitted.set_emits(name_emitted)
-            #Case Process
-            if(process!=None and subworkflow==None):
-                emitted = Emitted(name=full_code, origin=self.origin, emitted_by=process)
-                #TODO -> analyse the outputs of the process
-
-            if(process==None and subworkflow==None):
-                if(name_called[:5]=="Call_"):
-                    name_called = self.calls[name_called].get_code()
-                raise BioFlowInsightError(f"The call for '{name_called}' coudn't be found, before its use in the operation '{self.get_code(get_OG=True)}'{self.get_string_line(self.get_code(get_OG=True))}. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.", num =8, origin=self)
-
-            emitted.add_sink(self)
-            self.origins.append(emitted)
+        #Check that it not already been added
+        added = False
+        for o in self.origins:
+            if(full_code==o.get_code()):
+                added = True
+
+        if(not added):
+            #full_code, name_called, name_emitted = match.group(1), match.group(2), match.group(3)
+            IGNORE_NAMES = ['params']
+            #In the cas an operator is extracted at the end of the emit
+            if(full_code.count('.')>=2):
+                splited = full_code.split('.')
+                if( splited[-1] in constant.LIST_OPERATORS):
+                    full_code = '.'.join(splited[:-1])
+            if(name_called not in IGNORE_NAMES):
+                process = self.origin.get_process_from_name(name_called)
+                subworkflow = self.origin.get_subworkflow_from_name(name_called)
+
+                if(process!=None and subworkflow!=None):
+                    raise Exception(f"Problem in get_element -> {name_called} exists as process and subworkflow")
+                #Case subworkflow
+                if(process==None and subworkflow!=None):
+                    emitted = Emitted(name=full_code, origin=self.origin, emitted_by=subworkflow)
+                    emitted.set_emits(name_emitted)
+                #Case Process
+                if(process!=None and subworkflow==None):
+                    emitted = Emitted(name=full_code, origin=self.origin, emitted_by=process)
+                    #TODO -> analyse the outputs of the process
+
+                if(process==None and subworkflow==None):
+                    if(name_called[:5]=="Call_"):
+                        name_called = self.calls[name_called].get_code()
+                    raise BioFlowInsightError(f"The call for '{name_called}' coudn't be found, before its use in the operation '{self.get_code(get_OG=True)}'{self.get_string_line(self.get_code(get_OG=True))}. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.", num =8, origin=self)
+
+                emitted.add_sink(self)
+                self.origins.append(emitted)
 
     #This methods checks if the input is an emit and adds it if it's the case, it also returns T/F if it's an emit
     def check_is_emit(self, name):
@@ -171,28 +178,35 @@ class Operation(Executor):
             channel.add_source(self)
 
     def add_origin(self, name):
-        if(self.origin.get_DSL()=="DSL2"):
-            #Case it's a call and it's been replaced
-            if(re.fullmatch(constant.CALL_ID, name)):
-                self.origins.append(self.calls[name])
+        #Check that it's not already been added
+        added = False
+        for o in self.origins:
+            if(name==o.get_code()):
+                added = True
+
+        if(not added):
+            if(self.origin.get_DSL()=="DSL2"):
+                #Case it's a call and it's been replaced
+                if(re.fullmatch(constant.CALL_ID, name)):
+                    self.origins.append(self.calls[name])
+                else:
+                    ##Case it's a subworkflow
+                    #subworkflow = self.origin.get_subworkflow_from_name(name)
+                    #process = self.origin.get_process_from_name(name)
+                    #if(subworkflow!=None):
+                    #    print("George it's a subworkflow")
+                    #    #Case suborkflow
+                    #    self.origins.append(subworkflow)
+                    ##Case process
+                    #elif(process!=None):
+                    #    print("George it's a process")
+                    #    #Case process
+                    #    self.origins.append(process)
+                    ##In this case it's a channel
+                    #else:
+                    self.add_origin_channel(name)
             else:
-                ##Case it's a subworkflow
-                #subworkflow = self.origin.get_subworkflow_from_name(name)
-                #process = self.origin.get_process_from_name(name)
-                #if(subworkflow!=None):
-                #    print("George it's a subworkflow")
-                #    #Case suborkflow
-                #    self.origins.append(subworkflow)
-                ##Case process
-                #elif(process!=None):
-                #    print("George it's a process")
-                #    #Case process
-                #    self.origins.append(process)
-                ##In this case it's a channel
-                #else:
                 self.add_origin_channel(name)
-        else:
-            self.add_origin_channel(name)
                 
 
     #Function that from an operation gives the origin ('input') channels

src/process.py

@@ -75,6 +75,7 @@ class Process(Nextflow_Building_Blocks):
     def get_nb_outputs(self):
         return len(self.outputs)
     
+    #TODO -> Have a much better way of doing this  
     def extract_tools(self):
         script = self.script_code.lower()
         for tool in constant.TOOLS:

src/ro_crate.py

@@ -105,7 +105,7 @@ class RO_Crate:
             return f"{year}-{month}-{day}"
         return None
     
-
+    #TODO -> update this -> it's incomplet
     def get_url(self, file):
         if(self.workflow.dico!={}):
             return f"https://github.com/{self.workflow.get_address()}/blob/main/{file}"
@@ -114,8 +114,8 @@ class RO_Crate:
 
     def get_creators(self, file):
         info = self.fill_log_file(file, reverse = True)
-        for match in re.finditer(r"Author: ([ \w-]+) <([^>]+)>", info):
-            return [{"@id": match.group(1)}]
+        for match in re.finditer(r"Author: ([^>]+)<([^>]+)>",info):
+            return [{"@id": match.group(1).strip()}]
         return None
 
 

src/workflow.py

@@ -134,8 +134,8 @@ class Workflow:
     def get_authors(self):
         if(self.authors==None):
             authors = {}
-            for match in re.finditer(r"Author: ([ \w-]+) <([^>]+)>",self.log):
-                authors[match.group(2)] = match.group(1)
+            for match in re.finditer(r"Author: ([^>]+)<([^>]+)>",self.log):
+                authors[match.group(2)] = match.group(1).strip()
             tab = []
             for author in authors:
                 #tab.append({"@id":author, "name":authors[author]})