Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
BioFlow-Insight
Manage
Activity
Members
Labels
Plan
Issues
0
Issue boards
Milestones
Wiki
Code
Merge requests
1
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Package Registry
Model registry
Operate
Environments
Terraform modules
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
shareFAIR
BioFlow-Insight
Commits
c2fde659
Commit
c2fde659
authored
7 months ago
by
George Marchment
Browse files
Options
Downloads
Patches
Plain Diff
check if the relevant processes exist in workflow
parent
2cb08b6b
No related branches found
No related tags found
No related merge requests found
Pipeline
#14116
passed with stage
in 2 minutes and 19 seconds
Changes
2
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
src/bioflowinsighterror.py
+1
-0
1 addition, 0 deletions
src/bioflowinsighterror.py
src/workflow.py
+7
-0
7 additions, 0 deletions
src/workflow.py
with
8 additions
and
0 deletions
src/bioflowinsighterror.py
+
1
−
0
View file @
c2fde659
...
@@ -42,6 +42,7 @@ class BioFlowInsightError(Exception):
...
@@ -42,6 +42,7 @@ class BioFlowInsightError(Exception):
#* [18] -> something is expected to be defined in a file but is not
#* [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
#* [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
#* [22] -> a subworkflow or process defined was defined badly
#* [24] -> The user gives a relevant process which isn't in the workflow
########################
########################
...
...
This diff is collapsed.
Click to expand it.
src/workflow.py
+
7
−
0
View file @
c2fde659
...
@@ -543,6 +543,13 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
...
@@ -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
)
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
):
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
.
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
)
self
.
nextflow_file
.
generate_user_view
(
relevant_processes
=
relevant_processes
,
render_graphs
=
render_graphs
,
processes_2_remove
=
self
.
tab_processes_2_remove
)
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment