From c2fde65994213b93947b543114500a62fae1644c Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Fri, 11 Oct 2024 15:50:16 +0200
Subject: [PATCH] check if the relevant processes exist in workflow
---
src/bioflowinsighterror.py | 1 +
src/workflow.py | 7 +++++++
2 files changed, 8 insertions(+)
diff --git a/src/bioflowinsighterror.py b/src/bioflowinsighterror.py
index 82c3a65..a948908 100644
--- a/src/bioflowinsighterror.py
+++ b/src/bioflowinsighterror.py
@@ -42,6 +42,7 @@ class BioFlowInsightError(Exception):
#* [18] -> something is expected to be defined in a file but is not
#* [20] -> The sibworkflow either emits nothing or to many values for a use in an operation
#* [22] -> a subworkflow or process defined was defined badly
+#* [24] -> The user gives a relevant process which isn't in the workflow
########################
diff --git a/src/workflow.py b/src/workflow.py
index 03e0146..310bcd4 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -543,6 +543,13 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
self.nextflow_file.generate_process_dependency_graph(render_graphs = render_graphs, processes_2_remove = self.tab_processes_2_remove)
def generate_user_view(self, relevant_processes = [], render_graphs = True):
+ #Check all relevat processes are in wf
+ workflow_processes = []
+ for p in self.get_processes_called():
+ workflow_processes.append(p.get_name())
+ for p in relevant_processes:
+ if(p not in workflow_processes):
+ raise BioFlowInsightError(f"Process {p} given in relevant processes is not present in the workflow's processes", 24)
self.iniatilise_tab_processes_2_remove()
self.nextflow_file.generate_user_view(relevant_processes = relevant_processes, render_graphs = render_graphs, processes_2_remove = self.tab_processes_2_remove)
--
GitLab