diff --git a/src/code_.py b/src/code_.py
index fb3400143058bdf54d6c08c6f12c2609c4128864..c59e14d0359891c4d1719d9273c0c223845089c9 100644
--- a/src/code_.py
+++ b/src/code_.py
@@ -148,25 +148,32 @@ class Code:
for match in re.finditer(pattern, code):
connector = match.group(1)
start_map, end = match.span(0)
+ new = f"¤{id(self)}_{index}¤"
if(end_char=="{"):
end_map = extract_curly(code, end)
old = code[end:end_map-1]
+ new_code = f"{connector}{word}_modified {{ {new} }}"
else:
+ new_code = f"{connector}{word}_modified ({new})"
old = get_code_until_parenthese_count(code[end:], -1)
end_map = end+len(old)
old = old.strip()[:-1]
- new = f"¤{id(self)}_{index}¤"
- self.add_map_element(old, new)
+
+ if(old[:-1].strip()!=''):
+ self.add_map_element(old, new)
- old_code = code[start_map:end_map]
- new_code = f"{connector}{word}_modified {{ {new} }}"
- code = code.replace(old_code, new_code)
+ old_code = code[start_map:end_map]
+
+ temp =code
+ code = code.replace(old_code, new_code)
+ if(old_code!=new_code and code==temp):
+ raise Exception("The code was no updated")
- searching = True
- index+=1
- break
+ searching = True
+ index+=1
+ break
#For reduce
- for match in re.finditer(r"(\.|\|)\s*reduce[^{]+{", code):
+ for match in re.finditer(r"(\.|\|)\s*reduce\s+\{", code):
connector = match.group(1)
start_map, end = match.span(0)
end_map = extract_curly(code, end)
@@ -175,7 +182,10 @@ class Code:
self.add_map_element(old, new)
old_code = code[start_map:end_map]
new_code = f"{connector}reduce_modified {{ {new} }}"
+ temp =code
code = code.replace(old_code, new_code)
+ if(old_code!=new_code and code==temp):
+ raise Exception("The code was no updated")
searching = True
index+=1
break
@@ -183,7 +193,6 @@ class Code:
if(timeout>=constant.WHILE_UPPER_BOUND):
raise BioFlowInsightError(f"The WHILE_UPPER_BOUND was exceeded. BioFlow-Insight was unable to extract the inside of a 'map' operator. Make sure the workflow uses correct Nextflow syntaxe (https://www.nextflow.io/docs/latest/index.html).", type="Unable to extract the inside of a 'map' operator")
-
return code
def add_to_ternary_operation_dico(self, old, new):
diff --git a/src/graph.py b/src/graph.py
index 15930408acb990e3886195e4f2590091fcce4b09..6be771ce09be2957d0f6747148957634f4d49fa7 100644
--- a/src/graph.py
+++ b/src/graph.py
@@ -285,8 +285,8 @@ class Graph():
for sub in dico['subworkflows']:
add_edges_flow_edges(dico["subworkflows"][sub], added_in_condition)
- if(self.workflow.get_duplicate_status()):
- #if(False):#Right now not generating the colored edges
+ #if(self.workflow.get_duplicate_status()):
+ if(False):#Right now not generating the colored edges
checking_conditions = True
most_influential_conditions = self.workflow.get_most_influential_conditions()
list_most_influential_conditions = list(most_influential_conditions.keys())
diff --git a/src/outils.py b/src/outils.py
index 6d23850a316cd3111b14b260f44c7fa410048a3e..a69da0eb919dced0f258fc756b1e1688d6427bed 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -1495,7 +1495,10 @@ def extract_tools(script, extract_general_tools = False):
searching = False
for match in re.finditer(r'\'', script):
start, end = match.span(0)
- end = extract_single_quote(script+"\n\n\n\n", start+1)
+ try:
+ end = extract_single_quote(script+"\n\n\n\n", start+1)
+ except:
+ break
inside_single_quote = script[start:end]
script = script.replace(inside_single_quote, "")
searching = True
@@ -1507,7 +1510,10 @@ def extract_tools(script, extract_general_tools = False):
searching = False
for match in re.finditer(r'\"', script):
start, end = match.span(0)
- end = extract_double_quote(script+"\n\n\n\n", start+1)
+ try:
+ end = extract_double_quote(script+"\n\n\n\n", start+1)
+ except:
+ break
inside_double_quote = script[start:end]
script = script.replace(inside_double_quote, "")
searching = True
diff --git a/src/workflow.py b/src/workflow.py
index 878d5652d49339780ba15a59144952b39e6187d8..5a48035ffa6aa984d16fdf159d49af1501f5c7fa 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -680,8 +680,13 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
processes_called = self.get_processes_called()
number_processes_called = len(processes_called)
processes_2_tools = {}
+ print("Extracting the tools from the processes")
+ print('-'*len(processes_called)+">")
for p in processes_called:
+ print('.', end='')
processes_2_tools[p.get_code()] = p.get_tools()
+ print("\n")
+ print("Testing different combinations")
print('-'*number_of_tries+">")
for i in range(number_of_tries):
print('.', end='')
@@ -731,12 +736,12 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
if(len(cluster_organisation)>=reduction_alpha*number_processes_called and
len(cluster_organisation)<=reduction_beta*number_processes_called and
score<min_score):
- print()
- print("concordance", np.max(np.array(tab_nb_conditions_per_cluster)/np.array(tab_nb_executors_per_cluster)) )
- print("uniformity", (uniformity_variance / number_processes_called) )
- print("min_nb_clusters", (nb_clusters / number_processes_called) )
- print("min_nb_non_relevant_cluster", (nb_non_relevant_clusters / nb_clusters))
- print("score", score)
+ #print()
+ #print("concordance", np.max(np.array(tab_nb_conditions_per_cluster)/np.array(tab_nb_executors_per_cluster)) )
+ #print("uniformity", (uniformity_variance / number_processes_called) )
+ #print("min_nb_clusters", (nb_clusters / number_processes_called) )
+ #print("min_nb_non_relevant_cluster", (nb_non_relevant_clusters / nb_clusters))
+ #print("score", score)
min_processes = random_relevant_processes
min_score = score
return min_processes
@@ -1036,9 +1041,9 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#code = code.replace(old, new)
code = replace_group1(code, fr"({re.escape(old)})[^\w]", new)
if(temp_code==code):
- #print(code)
- #print("old", f'"{old}"')
- #print("new", f'"{new}"')
+ print(code)
+ print("old", f'"{old}"')
+ print("new", f'"{new}"')
raise Exception("Something went wrong: The code hasn't changed")
return code