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Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 03 Oct 2020 12:00:25 +0200
Description: run_resfinder.py is in PATH
--- a/tests/deprecated/functional_tests.py
+++ b/tests/deprecated/functional_tests.py
@@ -69,7 +69,7 @@
# She therefore runs resfinder cmd line.
# First Maria checks out the documentation.
- procs = run("python3 ../run_resfinder.py -h", shell=True, stdout=PIPE,
+ procs = run("run_resfinder.py -h", shell=True, stdout=PIPE,
check=True)
output = procs.stdout.decode()
self.assertIn("--help", output)
@@ -80,7 +80,7 @@
test1_dir = run_test_dir + "/" + test_names[0]
os.makedirs(test1_dir)
# Then she runs run_resfinder with her first isolate.
- cmd_acquired = ("python3 " + self.dir_res + "/run_resfinder.py"
+ cmd_acquired = ("run_resfinder.py"
+ " -ifa " + test_data[test_names[0]]
+ " -o " + test1_dir
+ " -s 'Escherichia coli'"
@@ -138,7 +138,7 @@
os.makedirs(test2_dir, exist_ok=False)
# Then she runs run_resfinder with her first isolate.
- cmd_acquired = ("python3 " + self.dir_res + "/run_resfinder.py"
+ cmd_acquired = ("run_resfinder.py"
+ " -ifq " + test_data[test_names[1]]
+ " -o " + test2_dir
+ " -s 'Escherichia coli'"
@@ -195,7 +195,7 @@
os.makedirs(test3_dir)
# Then she runs run_resfinder with her first isolate.
- cmd_point = ("python3 " + self.dir_res + "/run_resfinder.py"
+ cmd_point = ("run_resfinder.py"
+ " -ifa " + test_data[test_names[2]]
+ " -o " + test3_dir
+ " -s 'Escherichia coli'"
@@ -239,7 +239,7 @@
os.makedirs(test4_dir, exist_ok=False)
# Then she runs run_resfinder with her first isolate.
- cmd_acquired = ("python3 " + self.dir_res + "/run_resfinder.py"
+ cmd_acquired = ("run_resfinder.py"
+ " -ifq " + test_data[test_names[3]]
+ " -o " + test4_dir
+ " -s 'Escherichia coli'"
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