From 8317e93b8b887eac931695f427037125d0b5bd2e Mon Sep 17 00:00:00 2001
From: Bryan Brancotte <bryan.brancotte@pasteur.fr>
Date: Fri, 8 Mar 2024 15:07:08 +0100
Subject: [PATCH] transmit output_dir param, add test to prevent regression
---
src/workflow.py | 9 ++++++++-
tests/test_cli.py | 20 ++++++++++++++++++++
2 files changed, 28 insertions(+), 1 deletion(-)
create mode 100644 tests/test_cli.py
diff --git a/src/workflow.py b/src/workflow.py
index 5961369..3e04232 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -6,6 +6,7 @@ from . import constant
import os
import re
import json
+from pathlib import Path
class Workflow:
@@ -14,7 +15,13 @@ class Workflow:
license = None, creativeWorkStatus = None, authors = None,
version = None, keywords = None, producer = None,
publisher = None):
- self.nextflow_file = Nextflow_File(file, duplicate = duplicate, display_info = display_info)
+ self.nextflow_file = Nextflow_File(
+ file,
+ duplicate=duplicate,
+ display_info=display_info,
+ output_dir=output_dir
+ )
+ self.output_dir = Path(output_dir)
self.rocrate = None
self.name = name
self.datePublished = datePublished
diff --git a/tests/test_cli.py b/tests/test_cli.py
new file mode 100644
index 0000000..04db2ce
--- /dev/null
+++ b/tests/test_cli.py
@@ -0,0 +1,20 @@
+import pathlib
+import unittest
+from tempfile import TemporaryDirectory
+
+from bioflow_insight_cli.main import cli
+
+
+class TestCall(unittest.TestCase):
+
+ def test_cli_works(self):
+ cli("./wf_test/main.nf", render_graphs=True)
+ cli("./wf_test/main.nf", render_graphs=False)
+
+ def test_cli_output_considered(self):
+ with TemporaryDirectory() as my_temp_dir:
+ my_results = pathlib.Path(my_temp_dir) / "my_results"
+ self.assertFalse(my_results.exists())
+ cli("./wf_test/main.nf", render_graphs=False, output_dir=str(my_results))
+ self.assertTrue(my_results.exists(), "Results should be there, output_dir not taken into account")
+
--
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