diff --git a/src/graph.py b/src/graph.py
index 7252cb32fac66539d67797dc9c53c127f2a37663..925f15f5989aa30b5ceea892fbb689bcb56af0c4 100644
--- a/src/graph.py
+++ b/src/graph.py
@@ -292,11 +292,14 @@ class Graph():
def generate_user_view(self, relevant_processes = [], render_graphs = True):
#For now i'm only gonna work from the flattened dico
self.initialise_flattened_dico(self.dico_process_dependency_graph)
+ #self.initialise_flattened_dico(self.full_dico)
dico = self.dico_flattened
user_view = relev_user_view_builder(dico, relevant_modules=relevant_processes)
+
with open(self.get_output_dir()/ "graphs/user_view.json", 'w') as output_file :
json.dump(user_view, output_file, indent=4)
+
generate_graph(self.get_output_dir()/'graphs'/"user_view", user_view, label_edge=True, label_node=True, render_graphs = render_graphs)
diff --git a/src/outils_annotate.py b/src/outils_annotate.py
new file mode 100644
index 0000000000000000000000000000000000000000..0f968a8e48a7254dc72ad44b6ba60c386eadab6d
--- /dev/null
+++ b/src/outils_annotate.py
@@ -0,0 +1,201 @@
+import copy
+import numpy as np
+import re
+
+tools = []
+commands = []
+
+
+
+
+def get_propositions(process, tools = -1, commands = -1):
+ temp = []
+ if(tools!=-1):
+ for tool in tools:
+ #for character in char_after_tool:
+ for match in re.finditer(r"(\s|\(|\/|\|)"+tool+r"(\s|\-|\\|\.)", process):
+ #if(f"{tool}{character}" in process):
+ temp.append(tool)
+ if(commands!=-1):
+ for commands in commands:
+ tool, command = commands.split()
+ command = command.replace('+', '\+')
+ for match in re.finditer(tool+r"\s+\-[^\s]+\s+"+command, process):
+ temp.append(commands)
+ for match in re.finditer(tool+r"\s+"+command, process):
+ temp.append(commands)
+ for match in re.finditer(tool+r"\s+\\\s+"+command, process):
+ temp.append(commands)
+ for match in re.finditer(tool+r"\s+\-[^\s]+\s+[^\s]+\s+"+command, process):
+ temp.append(commands)
+ for match in re.finditer(tool+r"\.\w+\s+"+command, process):
+ temp.append(commands)
+ for match in re.finditer(tool+r"\.jar\s+[^\s]+\s+"+command, process):
+ temp.append(commands)
+
+ return list(set(temp))
+
+
+def get_propositions_from_user():
+ propositions = []
+ nb_prop = 1
+ input_val = "a"
+ while(input_val!=""):
+ input_val = input(f"Proposition {nb_prop} : ")
+ if(input_val!=""):
+ propositions.append(input_val)
+ nb_prop+=1
+ return propositions
+
+def print_colored_words(text, words):
+ temp_words = []
+ for word in words:
+ temp_words+= word.split()
+ words = temp_words
+
+ colors = ['\033[31m', '\033[32m', '\033[33m', '\033[34m', '\033[35m', '\033[36m'] # Colors: Red, Green, Yellow, Blue, Magenta, Cyan
+ color_index = 0
+
+ for i in range(len(words)):
+ word = words[i]
+ color = colors[color_index % len(colors)]
+ text = text.replace(word, f"{color}{word}\033[0m")
+ color_index += 1
+ print(text)
+
+def get_tools_commands_from_user_for_process(p, exiting_tools, existing_commands):
+ tools_found, commands_found = [], []
+ codes = []
+ codes.append(p.get_code())
+ 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("\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) : ")
+ tools_found += 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) : ")
+ commands_found += propositions
+
+ exiting_tools+= tools_found
+ existing_commands+= commands_found
+ 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/outils_graph.py b/src/outils_graph.py
index fc5d4c67f458e8842ee3abaf2e30779eb8873009..4f17a58cc4d36d3cf8a949a7430345dc79b55694 100644
--- a/src/outils_graph.py
+++ b/src/outils_graph.py
@@ -414,19 +414,24 @@ def get_neighbors(edges, A):
Bs.append(e['B'])
return Bs
-def exist_path(A, B, edges):
- N = get_nodes_from_edges(edges=edges)
- visited = {}
- for n in N:
- visited[n] = False
+
+def exist_path_rec(A, B, edges, visited):
visited[A] = True
if(A==B):
return True
for neigh in get_neighbors(edges, A):
- if(exist_path(neigh, B, edges)):
- return True
+ if(not visited[neigh]):
+ if(exist_path_rec(neigh, B, edges, visited = visited)):
+ return True
return False
+def exist_path(A, B, edges):
+ N = get_nodes_from_edges(edges=edges)
+ visited = {}
+ for n in N:
+ visited[n] = False
+ return exist_path_rec(A, B, edges, visited)
+
def nr_path_succ(n, r, dico, R):
rest_of_R = set(R)-set([r])
@@ -533,6 +538,7 @@ def relev_user_view_builder(dico, relevant_modules):
R = []
for r in relevant_modules:
R+=get_id_from_name(dico, r)
+ R = list(set(R))
outputs = get_output_nodes(dico)
inputs = get_input_nodes(dico)
#dico['nodes'].append({'id':"input", 'name':"input"})
diff --git a/src/workflow.py b/src/workflow.py
index 77ccd87a1b807159df1b7ad9003095625aed40c9..96bc4bbd22c19f73f24c66547e9336bae1152eee 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -4,6 +4,7 @@ from .nextflow_file import Nextflow_File
from .ro_crate import RO_Crate
from . import constant
from .outils_graph import flatten_dico, initia_link_dico_rec, get_number_cycles
+from .outils_annotate import get_tools_commands_from_user_for_process
from .bioflowinsighterror import BioFlowInsightError
#Outside packages
@@ -46,7 +47,8 @@ class Workflow:
version = None, keywords = None, producer = None,
publisher = None, processes_2_remove = None,
processes_annotation = None,
- personnal_acces_token = None):
+ personnal_acces_token = None,
+ processes_2_tools = None):
if(not os.path.isfile(file)):
nextflow_files = glob.glob(f'{file}/*.nf')
@@ -83,6 +85,7 @@ class Workflow:
self.producer = producer
self.publisher = publisher
self.personnal_acces_token = personnal_acces_token
+ self.processes_2_tools = processes_2_tools
if(processes_2_remove==""):
processes_2_remove = None
self.processes_2_remove = processes_2_remove
@@ -532,4 +535,21 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
temp = self.processes_2_remove.split(",")
for t in temp:
tab_processes_2_remove.append(t.strip())
- self.nextflow_file.generate_user_view(relevant_processes = relevant_processes, render_graphs = render_graphs, processes_2_remove = tab_processes_2_remove)
\ No newline at end of file
+ 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):
+ exiting_tools, existing_commands = [], []
+ processes = self.get_processes_used()
+ dico = {}
+ for p in processes:
+ 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
+ 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)
+ return self.processes_2_tools
+ else:
+ return self.processes_2_tools