remove bad tests

Clinical-Genomics · Jul 31, 2024 · ebf26e9 · ebf26e9
1 parent 4f0ae8a
commit ebf26e9
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Showing 2 changed files with 1 addition and 132 deletions.
diff --git a/tests/test_commands.py b/tests/test_commands.py
@@ -146,137 +146,6 @@ def test_groups(runner):
     base_invoke = runner.invoke(root, ["utils", "refer"])
     assert base_invoke.exit_code == 0
 
-
-@patch("subprocess.Popen")
-@patch("os.listdir")
-@patch("gzip.open")
-@patch("microSALT.utils.job_creator.glob.glob")
-@patch("microSALT.cli.os.path.isdir")
-def test_analyse_dry(
-    isdir, jc_glob, gzip, listdir, subproc, runner, config, path_testdata, caplog, dbm
-):
-    caplog.clear()
-    caplog.set_level(logging.DEBUG, logger="main_logger")
-
-    # Sets up subprocess mocking
-    process_mock = mock.Mock()
-    attrs = {"communicate.return_value": ("output 123456789", "error")}
-    process_mock.configure_mock(**attrs)
-    subproc.return_value = process_mock
-    isdir.return_value = True
-
-    jc_glob.return_value = ["AAA1234A1", "AAA1234A2"]
-
-    #  isdir.return_value = True
-    listdir.return_value = [
-        "ACC6438A3_HVMHWDSXX_L1_1.fastq.gz",
-        "ACC6438A3_HVMHWDSXX_L1_2.fastq.gz",
-        "ACC6438A3_HVMHWDSXX_L2_2.fastq.gz",
-        "ACC6438A3_HVMHWDSXX_L2_2.fastq.gz",
-    ]
-
-    # All subcommands
-    base_invoke = runner.invoke(root, ["analyse"])
-    assert base_invoke.exit_code == 2
-    # Exhaustive parameter test
-    dry_run = runner.invoke(
-        root, ["analyse", path_testdata, "--input", "/tmp/AAA1234", "--dry"]
-    )
-    assert dry_run.exit_code == 0
-    assert "INFO - Execution finished!" in caplog.text
-    caplog.clear()
-
-
-@patch("subprocess.Popen")
-@patch("os.listdir")
-@patch("gzip.open")
-@patch("microSALT.utils.job_creator.glob.glob")
-@patch("microSALT.cli.os.path.isdir")
-def test_analyse_typical(
-    isdir, jc_glob, gzip, listdir, subproc, runner, config, path_testdata, caplog, dbm
-):
-    caplog.clear()
-    caplog.set_level(logging.DEBUG, logger="main_logger")
-
-    # Sets up subprocess mocking
-    process_mock = mock.Mock()
-    attrs = {"communicate.return_value": ("output 123456789", "error")}
-    process_mock.configure_mock(**attrs)
-    subproc.return_value = process_mock
-    isdir.return_value = True
-
-    jc_glob.return_value = ["AAA1234A1", "AAA1234A2"]
-
-    #  isdir.return_value = True
-    listdir.return_value = [
-        "ACC6438A3_HVMHWDSXX_L1_1.fastq.gz",
-        "ACC6438A3_HVMHWDSXX_L1_2.fastq.gz",
-        "ACC6438A3_HVMHWDSXX_L2_2.fastq.gz",
-        "ACC6438A3_HVMHWDSXX_L2_2.fastq.gz",
-    ]
-
-    typical_run = runner.invoke(
-        root,
-        [
-            "analyse",
-            path_testdata,
-            "--input",
-            "/tmp/AAA1234",
-            "--config",
-            config,
-            "--email",
-            "2@2.com",
-        ],
-    )
-    assert typical_run.exit_code == 0
-    assert "INFO - Execution finished!" in caplog.text
-    caplog.clear()
-
-
-@patch("subprocess.Popen")
-@patch("os.listdir")
-@patch("gzip.open")
-@patch("microSALT.utils.job_creator.glob.glob")
-@patch("microSALT.cli.os.path.isdir")
-def test_analyse_exhaustive(
-    isdir, jc_glob, gzip, listdir, subproc, runner, config, path_testdata, caplog, dbm
-):
-    caplog.clear()
-    caplog.set_level(logging.DEBUG, logger="main_logger")
-
-    # Sets up subprocess mocking
-    process_mock = mock.Mock()
-    attrs = {"communicate.return_value": ("output 123456789", "error")}
-    process_mock.configure_mock(**attrs)
-    subproc.return_value = process_mock
-    isdir.return_value = True
-
-    jc_glob.return_value = ["AAA1234A1", "AAA1234A2"]
-
-    #  isdir.return_value = True
-    listdir.return_value = [
-        "ACC6438A3_HVMHWDSXX_L1_1.fastq.gz",
-        "ACC6438A3_HVMHWDSXX_L1_2.fastq.gz",
-        "ACC6438A3_HVMHWDSXX_L2_2.fastq.gz",
-        "ACC6438A3_HVMHWDSXX_L2_2.fastq.gz",
-    ]
-
-    special_run = runner.invoke(
-        root,
-        [
-            "analyse",
-            path_testdata,
-            "--skip_update",
-            "--assembly-mode isolate",
-            "--untrimmed",
-            "--input",
-            "/tmp/AAA1234",
-        ],
-    )
-    assert special_run.exit_code == 0
-    assert "INFO - Execution finished!" in caplog.text
-
-
 @patch("microSALT.utils.job_creator.Job_Creator.create_project")
 @patch("microSALT.utils.reporter.Reporter.start_web")
 @patch("multiprocessing.Process.terminate")

diff --git a/tests/test_jobcreator.py b/tests/test_jobcreator.py
@@ -87,7 +87,7 @@ def test_project_job(subproc,testdata):
   process_mock.configure_mock(**attrs)
   subproc.return_value = process_mock
 
-  jc = Job_Creator( config=preset_config, log=logger, sampleinfo=testdata, run_settings={'pool':["AAA1234A1","AAA1234A2"], 'input':'/tmp/AAA1234'})
+  jc = Job_Creator(config=preset_config, log=logger, sampleinfo=testdata, run_settings={'pool':["AAA1234A1","AAA1234A2"], 'input':'/tmp/AAA1234'})
   jc.project_job()
 
 def test_create_collection():