diff --git a/src/outils_annotate.py b/src/outils_annotate.py
index 0f968a8e48a7254dc72ad44b6ba60c386eadab6d..810b78c28a4e220023232ee1384ac2353457b961 100644
--- a/src/outils_annotate.py
+++ b/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
-
-
diff --git a/src/workflow.py b/src/workflow.py
index 96bc4bbd22c19f73f24c66547e9336bae1152eee..3fa3c1fac4e23bd6c26db8b9489f3ee007725eec 100644
--- a/src/workflow.py
+++ b/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)