update

src/outils_annotate.py

@@ -17,8 +17,8 @@ def get_propositions(process, tools = -1, commands = -1):
                 #if(f"{tool}{character}" in process):
                 temp.append(tool)
     if(commands!=-1):
-        for commands in commands:
-            tool, command = commands.split()
+        for c in commands:
+            tool, command = c.split()
             command = command.replace('+', '\+')
             for match in re.finditer(tool+r"\s+\-[^\s]+\s+"+command, process):
                 temp.append(commands)
@@ -70,7 +70,7 @@ def get_tools_commands_from_user_for_process(p, exiting_tools, existing_commands
     codes+=p.get_external_scripts_code()
 
     for c in codes:
-        print_colored_words(c, get_propositions(p, commands=existing_commands)+get_propositions(p, tools=exiting_tools))
+        print_colored_words(c, get_propositions(c, commands=existing_commands)+get_propositions(c, tools=exiting_tools))
         print("\nTOOLS")
         confirmation = 'a'
         while(confirmation!=""):
@@ -89,113 +89,3 @@ def get_tools_commands_from_user_for_process(p, exiting_tools, existing_commands
     return tools_found, commands_found, exiting_tools, existing_commands
 
 
-
-
-index = 0
-for process_id in process_2_annotations_pre_verification:
-    p = process_2_annotations_pre_verification[process_id]["process"]
-    try:
-        tmp = process_2_annotation[process_id]
-    except:
-        current_tools = process_2_annotations_pre_verification[process_id]["tools"]
-        current_commands = process_2_annotations_pre_verification[process_id]["commands"]
-
-        print(f"\n* Current progess : {index/len(process_2_annotations_pre_verification)*100:.2f}% ({len(process_2_annotations_pre_verification)-index} left)")
-        print("--------------------------------------------------")
-        print_colored_words(p, current_commands+current_tools+get_propositions(p, commands=commands)+get_propositions(p, tools=tools))
-        
-        validate_annoation = False
-        while(not validate_annoation):
-            print()
-            print_colored_words(f" - Current tools: {current_tools}", current_commands+current_tools)
-            print_colored_words(f" - Current commands: {current_commands}", current_commands+current_tools)
-            print()
-            annotation = input("Validate current annotations (press enter/ anykey otherwise):")
-            if(annotation==""):
-                validate_annoation = True
-            else:
-                print("\nTOOLS")
-                confirmation = 'a'
-                while(confirmation!=""):
-                    propositions = get_propositions_from_user()
-                    confirmation = input(f"Press 'ENTER' to validate this propostion of tools {propositions} (press any key otherwise) : ")
-                current_tools = propositions
-                print("\nCOMMANDS")
-                confirmation = 'a'
-                while(confirmation!=""):
-                    propositions = get_propositions_from_user()
-                    confirmation = input(f"Press 'ENTER' to validate this propostion of commands {propositions} (press any key otherwise) : ")
-                current_commands = propositions
-
-        tools+=current_tools
-        commands+=current_commands
-        tools = list(set(tools))
-        commands = list(set(commands))
-
-        ext_tools, ext_commands = [], []
-        for ext in process_2_annotations_pre_verification[process_id]["external_scripts"]:
-            envs = ["env python", "env Rscript"]
-            show_it = True
-            for env in envs:
-                if(env in ext):
-                    show_it = False
-
-            if(show_it):
-                print("\n--------------------------------------------------")
-                propositions = get_propositions(ext, tools=tools)
-                print_colored_words(ext, propositions)
-
-                print("\nTOOLS")
-                print_colored_words(f"Propositions are : {propositions}", propositions)
-                val = input("Press 'ENTER' to validate (press any key otherwise) : ")
-                if(val==''):
-                    ext_tools+=propositions
-                else:
-                    confirmation = 'a'
-                    while(confirmation!=""):
-                        propositions = get_propositions_from_user()
-                        confirmation = input(f"Press 'ENTER' to validate this propostion of tools {propositions} (press any key otherwise) : ")
-                    ext_tools+=propositions
-                
-                propositions = get_propositions(ext, commands=commands)
-                print_colored_words(ext, propositions)
-                print("\nCOMMANDS")
-                print_colored_words(f"Propositions are : {propositions}", propositions)
-                val = input("Press 'ENTER' to validate (press any key otherwise) : ")
-                if(val==''):
-                    ext_commands+=propositions
-                else:
-                    confirmation = 'a'
-                    while(confirmation!=""):
-                        propositions = get_propositions_from_user()
-                        confirmation = input(f"Press 'ENTER' to validate this propostion of commands {propositions} (press any key otherwise) : ")
-                    current_commands = propositions
-                    ext_commands+=propositions
-
-        current_tools+=ext_tools
-        current_commands+=ext_commands
-        current_tools = list(set(current_tools))
-        current_commands = list(set(current_commands))
-
-        tools+=current_tools
-        commands+=current_commands
-        tools = list(set(tools))
-        commands = list(set(commands))
-
-        process_2_annotation[process_id] = {}     
-        process_2_annotation[process_id]['process'] = process_2_annotations_pre_verification[process_id]['process']  
-        process_2_annotation[process_id]['has_external_scripts'] = process_2_annotations_pre_verification[process_id]['has_external_scripts']
-        process_2_annotation[process_id]['external_scripts'] = process_2_annotations_pre_verification[process_id]['external_scripts'] 
-        process_2_annotation[process_id]['R_modules'] = process_2_annotations_pre_verification[process_id]['R_modules']
-        process_2_annotation[process_id]['python_modules'] = process_2_annotations_pre_verification[process_id]['python_modules']
-        process_2_annotation[process_id]['perl_modules'] = process_2_annotations_pre_verification[process_id]['perl_modules']
-        process_2_annotation[process_id]['tools'] = current_tools
-        process_2_annotation[process_id]['commands'] = current_commands
-
-    with open("process_2_annotation.json", "w") as outfile:
-        json.dump(process_2_annotation, outfile, indent=4)
-
-
-    index+=1
-
-

src/workflow.py

@@ -49,7 +49,6 @@ class Workflow:
                  processes_annotation = None,
                  personnal_acces_token = None,
                  processes_2_tools = None):
-
         if(not os.path.isfile(file)):
             nextflow_files = glob.glob(f'{file}/*.nf')
             if(len(nextflow_files)==0):
@@ -538,15 +537,23 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
         self.nextflow_file.generate_user_view(relevant_processes = relevant_processes, render_graphs = render_graphs, processes_2_remove = tab_processes_2_remove)
 
     def build_processes_2_tools(self):
+        
         if(self.processes_2_tools==None):
+            print()
+            print("Let's extarct the tools from the processes")
+            print("------------------------------------------")
+            print()
             exiting_tools, existing_commands = [], []
-            processes = self.get_processes_used()
+            processes = self.get_processes_called()
             dico = {}
+            index=0
             for p in processes:
+                print(f"* {index/len(processes)*100:.2f}% ({index}) processes annotated")
                 tools_found, commands_found, exiting_tools, existing_commands = get_tools_commands_from_user_for_process(p, exiting_tools, existing_commands)
                 dico[p.get_code()] = {}
                 dico[p.get_code()]["tools"] = tools_found
                 dico[p.get_code()]["commands"] = commands_found
+                index+=1
             self.processes_2_tools = dico
             with open(f"{self.get_output_dir()}/processes_2_tools.json", 'w') as output_file :
                 json.dump(self.processes_2_tools, output_file, indent=2)