From d881ceff8c81a996340e8fd92c1df62603b792c8 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Mon, 31 Aug 2020 12:12:24 +0200
Subject: [PATCH] Add steps and test
Former-commit-id: e793a1ff7fc48c490c0d6eac8a3b76b1987ed741
---
steps/filter_ms_group.cwl | 57 +++++++++++++++++++++++++++++
test_workflow/empty_dirs/ms1/README | 0
test_workflow/empty_dirs/ms2/README | 0
test_workflow/empty_dirs/ms3/README | 0
test_workflow/empty_dirs/ms5/README | 0
test_workflow/filter_ms_group.json | 9 +++++
test_workflow/groups_spec.json | 4 ++
7 files changed, 70 insertions(+)
create mode 100644 steps/filter_ms_group.cwl
create mode 100644 test_workflow/empty_dirs/ms1/README
create mode 100644 test_workflow/empty_dirs/ms2/README
create mode 100644 test_workflow/empty_dirs/ms3/README
create mode 100644 test_workflow/empty_dirs/ms5/README
create mode 100644 test_workflow/filter_ms_group.json
create mode 100644 test_workflow/groups_spec.json
diff --git a/steps/filter_ms_group.cwl b/steps/filter_ms_group.cwl
new file mode 100644
index 00000000..51374067
--- /dev/null
+++ b/steps/filter_ms_group.cwl
@@ -0,0 +1,57 @@
+class: CommandLineTool
+cwlVersion: v1.0
+id: filter_ms_group
+baseCommand:
+ - python3
+arguments:
+ - position: 0
+ valueFrom: script.py
+inputs:
+ - id: group_id
+ type: string
+ - id: groups_specification
+ type: File
+ inputBinding:
+ position: 1
+ - id: measurement_sets
+ type: 'Directory[]'
+ inputBinding:
+ position: 2
+outputs:
+ - id: output
+ type: 'Directory[]?'
+ outputBinding:
+ loadContents: true
+ glob: selected_ms.json
+ outputEval: '$(JSON.parse(self[0].contents))'
+label: filter_ms_group
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: script.py
+ entry: |
+ import sys
+ import json
+ import os.path as path
+ group_id = "$(inputs.group_id)"
+ json_file = sys.argv[1]
+ ms_list = sys.argv[2:]
+
+ ms_by_name = { ms.split(path.sep)[-1]:
+ {'class':'Directory', 'path': ms} for ms in ms_list}
+
+ output_file = 'selected_ms.json'
+
+ with open(json_file, 'r') as f_stream:
+ selected_ms = json.load(f_stream)[group_id]
+ print(selected_ms, ms_by_name)
+ selected_ms = [ms_by_name[ms_name] for ms_name in selected_ms]
+
+
+ with open(output_file, 'w') as f_stream:
+ json.dump(selected_ms, f_stream)
+
+
+
diff --git a/test_workflow/empty_dirs/ms1/README b/test_workflow/empty_dirs/ms1/README
new file mode 100644
index 00000000..e69de29b
diff --git a/test_workflow/empty_dirs/ms2/README b/test_workflow/empty_dirs/ms2/README
new file mode 100644
index 00000000..e69de29b
diff --git a/test_workflow/empty_dirs/ms3/README b/test_workflow/empty_dirs/ms3/README
new file mode 100644
index 00000000..e69de29b
diff --git a/test_workflow/empty_dirs/ms5/README b/test_workflow/empty_dirs/ms5/README
new file mode 100644
index 00000000..e69de29b
diff --git a/test_workflow/filter_ms_group.json b/test_workflow/filter_ms_group.json
new file mode 100644
index 00000000..dbdcc347
--- /dev/null
+++ b/test_workflow/filter_ms_group.json
@@ -0,0 +1,9 @@
+{
+"group_id": "1",
+"groups_specification": {"class": "File", "path": "groups_spec.json"},
+"measurement_sets": [
+ {"class": "Directory", "path": "empty_dirs/ms1"},
+ {"class": "Directory", "path": "empty_dirs/ms2"},
+ {"class": "Directory", "path": "empty_dirs/ms3"},
+ {"class": "Directory", "path": "empty_dirs/ms5"}]
+}
diff --git a/test_workflow/groups_spec.json b/test_workflow/groups_spec.json
new file mode 100644
index 00000000..89e56a1f
--- /dev/null
+++ b/test_workflow/groups_spec.json
@@ -0,0 +1,4 @@
+{
+ "1": ["ms1", "ms2"],
+ "2": ["ms3", "ms5"]
+}
--
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