From c2123ddde2f035fa9ef27acb8dbc0d408ddc017f Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Tue, 19 Mar 2024 12:12:21 +0100
Subject: [PATCH] update
---
README.md | 2 +-
src/call.py | 3 +++
src/main_DSL2.py | 11 +++++++++++
src/nextflow_file.py | 19 +++++++++++++++++--
src/operation.py | 5 +++++
src/workflow.py | 25 +++++++++++++++++++++++++
6 files changed, 62 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index 3596897..42dbd76 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
# BioFlow-Insight
-[](https://www.gnu.org/licenses/gpl-3.0) []() [](https://zenodo.org/uploads/10818333)
+[](https://www.gnu.org/licenses/gpl-3.0) []()
diff --git a/src/call.py b/src/call.py
index 826778d..0ae3d38 100644
--- a/src/call.py
+++ b/src/call.py
@@ -53,6 +53,9 @@ class Call(Executor):
for para in self.parameters:
if(para.get_type()=="Call"):
tab = para.get_elements_called(tab_input = tab.copy(), first_call = False)
+ elif(para.get_type()=="Operation"):
+ tab += para.get_elements_called(tab = tab.copy())
+
temp = list(set(tab))
#del tab
return temp
diff --git a/src/main_DSL2.py b/src/main_DSL2.py
index cb82f41..e882493 100644
--- a/src/main_DSL2.py
+++ b/src/main_DSL2.py
@@ -42,6 +42,17 @@ class Main_DSL2(Nextflow_Building_Blocks):
def get_process_from_name(self, name):
return self.origin.get_process_from_name(name)
+ def get_processes_called(self, tab = []):
+
+ for c in self.get_all_called():
+ if(c.get_type()=="Process"):
+ tab.append(c)
+ elif(c.get_type()=="Subworkflow"):
+ tab+=c.get_processes_called()
+
+ return list(set(tab))
+
+
def get_function_from_name(self, name):
return self.origin.get_function_from_name(name)
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 740bd4e..f23e39a 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -295,8 +295,23 @@ class Nextflow_File(Nextflow_Building_Blocks):
return None
raise Exception(f"Process '{name}' couldn't be found in '{self.get_file_address()}'")
- def get_number_processes(self):
- return len(self.processes)
+
+ def get_processes_defined(self, tab = []):
+ tab+= super().get_processes()
+ for include in self.includes:
+ tab+=include.get_file().get_processes_defined()
+ return list(set(tab))
+
+
+ def get_processes_called(self, tab = []):
+ if(self.get_DSL()=="DSL1"):
+ return self.get_processes()
+ elif(self.get_DSL()=="DSL2"):
+ return self.main.get_processes_called()
+ else:
+ raise Exception("This shouldn't happen!")
+
+
#----------------------
diff --git a/src/operation.py b/src/operation.py
index 8f7b1e5..8927f0b 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -62,6 +62,11 @@ class Operation(Executor):
def add_channel(self, channel):
self.origin.add_channel(channel)
+ def get_elements_called(self, tab = []):
+ for o in self.origins:
+ if(o.get_type()=="Call"):
+ tab+=o.get_elements_called()
+ return tab
def add_origin_channel(self, name):
diff --git a/src/workflow.py b/src/workflow.py
index db2d7a3..f458b40 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -7,6 +7,10 @@ import os
import re
import json
from pathlib import Path
+import glob
+
+from .bioflowinsighterror import BioFlowInsightError
+
class Workflow:
@@ -15,6 +19,19 @@ class Workflow:
license = None, creativeWorkStatus = None, authors = None,
version = None, keywords = None, producer = None,
publisher = None, processes_2_remove = None):
+ print("here")
+ if(not os.path.isfile(file)):
+ nextflow_files = glob.glob(f'{file}/*.nf')
+ if(len(nextflow_files)==0):
+ raise BioFlowInsightError("No Nextflow files ('.nf') are in the directory!", num = -1)
+ try:
+ file = '/'.join(nextflow_files[0].split('/')[:-1])+"/main.nf"
+ with open(file, 'r') as f:
+ txt= f.read()
+ except:
+ file =nextflow_files[0]
+
+
self.nextflow_file = Nextflow_File(
file,
duplicate=duplicate,
@@ -207,6 +224,14 @@ class Workflow:
def add_2_rocrate(self, dico):
self.nextflow_file.add_2_rocrate(dico)
+ def get_processes_defined(self):
+ return self.nextflow_file.get_processes_defined()
+
+ def get_processes_called(self):
+ return self.nextflow_file.get_processes_called()
+
+
+
def initialise_rocrate(self):
self.rocrate = RO_Crate(self)
self.rocrate.initialise()
--
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