From d9a06fcf6ba90379ce47fb5662681053eba60d47 Mon Sep 17 00:00:00 2001
From: Bryan Brancotte <bryan.brancotte@pasteur.fr>
Date: Fri, 8 Mar 2024 15:53:13 +0100
Subject: [PATCH] sanitize workflow name to be usable as a filename
---
src/ro_crate.py | 6 +++++-
tests/test_cli.py | 10 +++++++++-
2 files changed, 14 insertions(+), 2 deletions(-)
diff --git a/src/ro_crate.py b/src/ro_crate.py
index 6330b41..22c1179 100644
--- a/src/ro_crate.py
+++ b/src/ro_crate.py
@@ -155,5 +155,9 @@ class RO_Crate:
self.fill_from_workflow()
self.dico.pop("temp_directory")
- with open(f"{self.workflow.get_output_dir()}/ro-crate-metadata-{self.workflow.get_name()}.json", 'w') as output_file :
+ name = self.workflow.get_name()
+ name = name.replace('github.com/', '')
+ name = re.sub(r"^[ .]|[/<>:\"\\|?*]+|[ .]$", "-", name)
+
+ with open(f"{self.workflow.get_output_dir()}/ro-crate-metadata-{name}.json", 'w') as output_file :
json.dump(self.dico, output_file, indent=2)
\ No newline at end of file
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 04db2ce..076721c 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -6,7 +6,6 @@ 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)
@@ -18,3 +17,12 @@ class TestCall(unittest.TestCase):
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")
+ def test_with_illegal_path_char_in_name(self):
+ with TemporaryDirectory() as my_temp_dir:
+ my_results = pathlib.Path(my_temp_dir) / "my_results"
+ cli(
+ "./wf_test/main.nf",
+ render_graphs=False,
+ output_dir=str(my_results),
+ name="https://github.com/blabla/toto:qsd!qsd%#sqdqsd"
+ )
--
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