diff --git a/src/graph.py b/src/graph.py
index ebbabe68cda82852735b517e266ddaa913323971..b9157e7844f30462f34b73e9e0053e32c8bd0cb2 100644
--- a/src/graph.py
+++ b/src/graph.py
@@ -15,12 +15,13 @@ class Graph():
#This dico give for the nodes its sister nodes
self.link_dico = None
#Dico to graph without operations
- self.dico_wo_operation = {}
+ self.dico_process_dependency_graph = {}
self.dico_wo_branch_operation = {}
#Dictionaries for metadata
#Dico flattened (without any subworkflows)
self.dico_flattened = {}
+ self.initialised = False
@@ -69,11 +70,15 @@ class Graph():
self.get_process_dependency_graph()
- #self.networkX_wo_operations = self.get_networkx_graph(self.dico_wo_operation, self.networkX_wo_operations)
+ #self.networkX_wo_operations = self.get_networkx_graph(self.dico_process_dependency_graph, self.networkX_wo_operations)
self.dico_flattened["nodes"] = []
self.dico_flattened["edges"] = []
#This will stay empty -> it's just so we can use the same function
self.dico_flattened["subworkflows"] = []
+ self.initialised = True
+
+ def is_initialised(self):
+ return self.initialised
def get_output_dir(self):
return self.workflow.get_output_dir()
@@ -130,11 +135,14 @@ class Graph():
def get_specification_graph_wo_orphan_operations_wo_labels(self, filename = "specification_wo_orphan_operations_wo_labels", render_graphs = True):
generate_graph(self.get_output_dir()/'graphs'/filename, graph_dico_wo_orphan_operations(self.full_dico), label_edge=False, label_node=False, render_graphs = render_graphs)
+ def get_process_dependency_graph_dico(self):
+ return self.dico_process_dependency_graph
+
def get_process_dependency_graph(self):
self.intia_link_dico()
#Function that replicates the workflow's structure wo the operations in the nodes
- def replicate_dico_wo_operations(dico_struct):
+ def replicate_dico_process_dependency_graphs(dico_struct):
dico = {}
dico['nodes'] = []
dico['edges'] = []
@@ -143,10 +151,10 @@ class Graph():
if(is_process(node['id'])):
dico['nodes'].append(node)
for sub in dico_struct['subworkflows']:
- dico['subworkflows'][sub] = replicate_dico_wo_operations(dico_struct['subworkflows'][sub])
+ dico['subworkflows'][sub] = replicate_dico_process_dependency_graphs(dico_struct['subworkflows'][sub])
return dico
- dico = replicate_dico_wo_operations(self.full_dico)
+ dico = replicate_dico_process_dependency_graphs(self.full_dico)
#This is a dictionnary which links every node to it's connected process
node_2_processes = copy.deepcopy(self.link_dico)
@@ -190,14 +198,14 @@ class Graph():
add_edges(dico)
- self.dico_wo_operation = dico
+ self.dico_process_dependency_graph = dico
with open(f"{self.get_output_dir()}/graphs/process_dependency_graph.json", 'w') as output_file :
- json.dump(self.dico_wo_operation, output_file, indent=4)
+ json.dump(self.dico_process_dependency_graph, output_file, indent=4)
def render_graph_wo_operations(self, filename = "process_dependency_graph", render_graphs = True):
- generate_graph(self.get_output_dir()/'graphs'/filename, self.dico_wo_operation, render_graphs = render_graphs, label_edge=False, label_node=False)
+ generate_graph(self.get_output_dir()/'graphs'/filename, self.dico_process_dependency_graph, render_graphs = render_graphs, label_edge=False, label_node=False)
def get_dependency_graph(self):
@@ -283,12 +291,14 @@ class Graph():
#============================
def initialise_flattened_dico(self, dico):
- for node in dico["nodes"]:
- self.dico_flattened["nodes"].append(node)
- for edge in dico["edges"]:
- self.dico_flattened["edges"].append(edge)
- for subworkflow in dico["subworkflows"]:
- self.initialise_flattened_dico(dico["subworkflows"][subworkflow])
+
+ flatten_dico(dico, self.dico_flattened)
+ #for node in dico["nodes"]:
+ # self.dico_flattened["nodes"].append(node)
+ #for edge in dico["edges"]:
+ # self.dico_flattened["edges"].append(edge)
+ #for subworkflow in dico["subworkflows"]:
+ # self.initialise_flattened_dico(dico["subworkflows"][subworkflow])
def get_metadata(self, graph):
G = self.get_networkx_graph(graph, None)
@@ -439,7 +449,7 @@ class Graph():
def get_metadata_process_dependency_graph(self):
- dico = self.get_metadata(self.dico_wo_operation)
+ dico = self.get_metadata(self.dico_process_dependency_graph)
with open(self.get_output_dir()/ "graphs/metadata_process_dependency_graph.json", 'w') as output_file :
json.dump(dico, output_file, indent=4)
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 1309305cc29772111dc606b6074ef7b0bb934b0a..a4a8cc4a8657c23b2f7d9d5ef1d3796c91933d22 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -692,6 +692,8 @@ class Nextflow_File(Nextflow_Building_Blocks):
self.graph.get_metadata_dependency_graph()
self.graph.get_metadata_process_dependency_graph()
+ def get_graph(self):
+ return self.graph
#def get_metadata_graph_wo_operations(self):
# self.graph.get_metadata_graph_wo_operations()
diff --git a/src/outils_graph.py b/src/outils_graph.py
index 95a931351ab64c0a6bf20652f43833c14dc2e46d..4f18d9abc6c840bbab06476172bdb989e8614f15 100644
--- a/src/outils_graph.py
+++ b/src/outils_graph.py
@@ -333,4 +333,14 @@ def get_longest_distance(graph):
# longest_path = longest_path["nb"]
# smallest_path = shortest_path["nb"]
#
-# return number_paths_source_2_sink, longest_path, smallest_path
\ No newline at end of file
+# return number_paths_source_2_sink, longest_path, smallest_path
+
+
+def flatten_dico(dico, dico_flattened):
+ for node in dico["nodes"]:
+ dico_flattened["nodes"].append(node)
+ for edge in dico["edges"]:
+ dico_flattened["edges"].append(edge)
+ for subworkflow in dico["subworkflows"]:
+ flatten_dico(dico["subworkflows"][subworkflow], dico_flattened)
+ return dico_flattened
\ No newline at end of file
diff --git a/src/workflow.py b/src/workflow.py
index 57c8686e87a63c04a42804777e833f7dcfd54972..da73fd34f4734120d5fae47a075a7fada7844bc3 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -2,6 +2,7 @@
from .nextflow_file import Nextflow_File
from .ro_crate import RO_Crate
from . import constant
+from .outils_graph import flatten_dico
import os
import re
@@ -261,7 +262,63 @@ class Workflow:
self.rocrate = RO_Crate(self)
self.rocrate.initialise()
+ def get_layers(self):
+ graph = self.nextflow_file.get_graph()
+ if(not graph.is_initialised()):
+ graph.initialise()
+ process_dependency_graph = graph.get_process_dependency_graph_dico()
+ dico_flattened = {"nodes": [], "edges": []}
+
+ def get_node(dico, id):
+ for n in dico['nodes']:
+ if(n['id']==id):
+ return n
+ return None
+ def remove_node(dico, id):
+ node = None
+ for n in dico['nodes']:
+ if(n['id']==id):
+ node = n.copy()
+ break
+ try:
+ dico['nodes'].remove(node)
+ except:
+ print("prob1")
+
+ def remove_edge_if_A(dico, id_A):
+ edges = []
+ for edge in dico['edges']:
+ if(edge['A']==id_A):
+ edges.append(edge)
+ for edge in edges:
+ try:
+ dico['edges'].remove(edge)
+ except:
+ print("prob2")
+
+ flatten_dico(process_dependency_graph, dico_flattened)
+ layers = []
+ while(dico_flattened["nodes"]!=[]):
+
+ layer = dico_flattened["nodes"].copy()
+
+ for edge in dico_flattened["edges"]:
+ try:
+ layer.remove(get_node(dico_flattened, edge['B']))
+ except:
+ None
+
+
+ for node in layer:
+ dico_flattened['nodes'].remove(node)
+ remove_edge_if_A(dico_flattened, node['id'])
+ layers.append(layer)
+
+
+ return layers
+
+ print(flatten_dico(process_dependency_graph, dico_flattened))
def initialise(self, create_rocrate = True):
self.nextflow_file.initialise()