From 270e473b8dc5e90b066c12534d251cbf86e55474 Mon Sep 17 00:00:00 2001
From: Tammo Jan Dijkema <dijkema@astron.nl>
Date: Thu, 31 Oct 2019 11:34:41 +0100
Subject: [PATCH] Rename parameters_input to steps
Former-commit-id: 42354972f756e457a4851cba0cd50adbaa7d4649
---
steps/DP3.AOFlaggerStepGenerator.cwl | 6 +++---
steps/DP3.AveragerStepGenerator.cwl | 2 +-
steps/DP3.DemixerStepGenerator.cwl | 6 +++---
steps/DP3.GenericStep.cwl | 8 ++++----
steps/DP3.ParsetGenerator.cwl | 20 ++++++++++----------
steps/DP3.PreflaggerStepGenerator.cwl | 2 +-
subworkflow/ndppp_prep_cal.cwl | 6 +++---
test_workflow/flag_average.cwl | 2 +-
8 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/steps/DP3.AOFlaggerStepGenerator.cwl b/steps/DP3.AOFlaggerStepGenerator.cwl
index 5b7b6ce9..58effb48 100755
--- a/steps/DP3.AOFlaggerStepGenerator.cwl
+++ b/steps/DP3.AOFlaggerStepGenerator.cwl
@@ -5,7 +5,7 @@ cwlVersion: v1.0
id: aoflagger_step_generator
inputs:
- - id: parameters_input
+ - id: steps
type: Any[]?
default: []
- id: step_name
@@ -95,8 +95,8 @@ steps:
default: 'aoflagger'
- id: step_id
source: step_name
- - id: parameters_input
- source: parameters_input
+ - id: steps
+ source: steps
- id: parameters
valueFrom: $(inputs)
- id: count.save
diff --git a/steps/DP3.AveragerStepGenerator.cwl b/steps/DP3.AveragerStepGenerator.cwl
index c75232c6..411efad2 100755
--- a/steps/DP3.AveragerStepGenerator.cwl
+++ b/steps/DP3.AveragerStepGenerator.cwl
@@ -60,7 +60,7 @@ steps:
default: 'averager'
- id: step_id
source: step_name
- - id: parameters_input
+ - id: steps
source: input_parset
- id: parameters
valueFrom: $(inputs)
diff --git a/steps/DP3.DemixerStepGenerator.cwl b/steps/DP3.DemixerStepGenerator.cwl
index c11ced07..24b3732a 100755
--- a/steps/DP3.DemixerStepGenerator.cwl
+++ b/steps/DP3.DemixerStepGenerator.cwl
@@ -7,7 +7,7 @@ $namespaces:
id: demix_step_generator
inputs:
- - id: parameters_input
+ - id: steps
type: Any[]?
default: []
- id: step_name
@@ -134,8 +134,8 @@ outputs:
steps:
- id: DP3_GenericStep
in:
- - id: parameters_input
- source: parameters_input
+ - id: steps
+ source: steps
- id: output_files
default: ["instrumentmodel"]
diff --git a/steps/DP3.GenericStep.cwl b/steps/DP3.GenericStep.cwl
index 28934bb7..a4e4149d 100755
--- a/steps/DP3.GenericStep.cwl
+++ b/steps/DP3.GenericStep.cwl
@@ -8,7 +8,7 @@ requirements:
- class: InlineJavascriptRequirement
inputs:
- - id: parameters_input
+ - id: steps
type: Any[]
- id: parameters
@@ -36,9 +36,9 @@ expression: |-
delete inputs.parameters.step_type;
delete inputs.parameters.step_id;
- delete inputs.parameters.parameters_input;
+ delete inputs.parameters.steps;
delete inputs.parameters.parameters;
- delete inputs.parameters.parameters_input;
+ delete inputs.parameters.steps;
var new_step = {'step_type': step_type,
@@ -47,7 +47,7 @@ expression: |-
'output_files': output_files};
- var in_parameters = inputs.parameters_input;
+ var in_parameters = inputs.steps;
// Checks if the step_id is duplicate if so raised an exception
var step_ids = []
diff --git a/steps/DP3.ParsetGenerator.cwl b/steps/DP3.ParsetGenerator.cwl
index c810ac8a..8cccf4cc 100644
--- a/steps/DP3.ParsetGenerator.cwl
+++ b/steps/DP3.ParsetGenerator.cwl
@@ -18,7 +18,7 @@ arguments:
true = True
false = False
null = None
- steps_list = $(inputs.parameters_input)
+ steps_list = $(inputs.steps)
steps_id_list = list(map(lambda item: item['step_id'], steps_list))
for step in steps_list:
@@ -50,7 +50,7 @@ arguments:
last_step_line = 'steps=[%s]' % ', '.join(steps_id_list)
print(last_step_line)
inputs:
- - id: parameters_input
+ - id: steps
type: Any[]?
outputs:
@@ -66,8 +66,8 @@ outputs:
outputEval: |-
${
var outfiles = []
- for(var step in inputs.parameters_input){
- step = inputs.parameters_input[step]
+ for(var step in inputs.steps){
+ step = inputs.steps[step]
for(var parameter in step['parameters']){
parameter = step['parameters'][parameter]
@@ -85,8 +85,8 @@ outputs:
outputEval: |
${
var outdirs = []
- for(var step in inputs.parameters_input){
- step = inputs.parameters_input[step]
+ for(var step in inputs.steps){
+ step = inputs.steps[step]
for(var parameter in step['parameters']){
parameter = step['parameters'][parameter]
if (parameter != null && parameter.class=='Directory'){
@@ -104,8 +104,8 @@ outputs:
outputEval: |
${
var out_names = {}
- for(var step_idx in inputs.parameters_input){
- var step = inputs.parameters_input[step_idx]
+ for(var step_idx in inputs.steps){
+ var step = inputs.steps[step_idx]
var step_id = step['step_id']
var step_dirs = {}
if(!step.hasOwnProperty("output_files")) continue;
@@ -129,8 +129,8 @@ outputs:
outputEval: |-
${
var out_names = {}
- for(var step_idx in inputs.parameters_input){
- var step = inputs.parameters_input[step_idx]
+ for(var step_idx in inputs.steps){
+ var step = inputs.steps[step_idx]
var step_id = step['step_id']
var step_dirs = {}
if(!step.hasOwnProperty("output_directories")) continue;
diff --git a/steps/DP3.PreflaggerStepGenerator.cwl b/steps/DP3.PreflaggerStepGenerator.cwl
index f7f59654..f3427fc8 100755
--- a/steps/DP3.PreflaggerStepGenerator.cwl
+++ b/steps/DP3.PreflaggerStepGenerator.cwl
@@ -181,7 +181,7 @@ steps:
default: 'preflagger'
- id: step_id
source: step_name
- - id: parameters_input
+ - id: steps
source: input_parset
- id: parameters
valueFrom: $(inputs)
diff --git a/subworkflow/ndppp_prep_cal.cwl b/subworkflow/ndppp_prep_cal.cwl
index 8226f13a..dda41c70 100644
--- a/subworkflow/ndppp_prep_cal.cwl
+++ b/subworkflow/ndppp_prep_cal.cwl
@@ -116,7 +116,7 @@ steps:
'sbg:y': -119.96077728271484
- id: aoflag
in:
- - id: parameters_input
+ - id: steps
source:
- flagedge/parameters_out
- id: step_name
@@ -148,7 +148,7 @@ steps:
'sbg:y': -44.651588439941406
- id: demixstepgenerator
in:
- - id: parameters_input
+ - id: steps
source:
- flagamp/parameters_out
out:
@@ -158,7 +158,7 @@ steps:
'sbg:y': 156.3474578857422
- id: parsetgenerator
in:
- - id: parameters_input
+ - id: steps
source:
- demix_select/output_arguments
out:
diff --git a/test_workflow/flag_average.cwl b/test_workflow/flag_average.cwl
index 09a0eb5f..ba872d9b 100644
--- a/test_workflow/flag_average.cwl
+++ b/test_workflow/flag_average.cwl
@@ -36,7 +36,7 @@ steps:
'sbg:y': -729
- id: parset_generator
in:
- - id: parameters_input
+ - id: steps
source:
- average_step_generator/parameters_out
out:
--
GitLab