nf-core · ErikDanielsson · Apr 8, 2021 · Apr 8, 2021 · Apr 8, 2021 · Apr 8, 2021
diff --git a/tests/lint/files_unchanged.py b/tests/lint/files_unchanged.py
@@ -0,0 +1,29 @@
+import pytest
+import shutil
+import tempfile
+import os
+
+import nf_core.lint
+
+
+def test_files_unchanged_pass(self):
+    self.lint_obj._load()
+    results = self.lint_obj.files_unchanged()
+    assert len(results.get("warned", [])) == 0
+    assert len(results.get("failed", [])) == 0
+    assert len(results.get("ignored", [])) == 0
+    assert not results.get("could_fix", True)
+
+
+def test_files_unchanged_fail(self):
+    failing_file = os.path.join(".github", "CONTRIBUTING.md")
+    new_pipeline = self._make_pipeline_copy()
+    with open(os.path.join(new_pipeline, failing_file), "a") as fh:
+        fh.write("THIS SHOULD NOT BE HERE")
+
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    results = lint_obj.files_unchanged()
+    assert len(results["failed"]) == 1
+    assert failing_file in results["failed"][0]
+    assert results["could_fix"]
diff --git a/tests/lint/nextflow_config.py b/tests/lint/nextflow_config.py
@@ -0,0 +1,54 @@
+import pytest
+import unittest
+import tempfile
+import os
+import shutil
+
+import nf_core.create
+import nf_core.lint
+
+
+def test_nextflow_config_example_pass(self):
+    """Tests that config variable existence test works with good pipeline example"""
+    self.lint_obj._load_pipeline_config()
+    result = self.lint_obj.nextflow_config()
+    assert len(result["failed"]) == 0
+    assert len(result["warned"]) == 0
+
+
+def test_nextflow_config_bad_name_fail(self):
+    """Tests that config variable existence test fails with bad pipeline name"""
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+
+    lint_obj.nf_config["manifest.name"] = "bad_name"
+    lint_obj.nf_config["process.container"] = "bad_name:dev"
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 1
+    assert len(result["warned"]) == 0
+
+
+def test_nextflow_config_bad_container_name_failed(self):
+    """Tests that config variable existence test fails with bad container name"""
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+
+    lint_obj.nf_config["process.container"] = "bad_name"
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 0
+    assert len(result["warned"]) == 1
+
+
+def test_nextflow_config_dev_in_release_mode_failed(self):
+    """Tests that config variable existence test fails with dev version in release mode"""
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+
+    lint_obj.release_mode = True
+    lint_obj.nf_config["manifest.version"] = "dev_is_bad_name"
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 1
+    assert len(result["warned"]) == 0
diff --git a/tests/test_lint.py b/tests/test_lint.py
@@ -202,6 +202,18 @@ def test_sphinx_rst_files(self):
 
     from lint.merge_markers import test_merge_markers_found
 
+    from lint.nextflow_config import (
+        test_nextflow_config_example_pass,
+        test_nextflow_config_bad_name_fail,
+        test_nextflow_config_bad_container_name_failed,
+        test_nextflow_config_dev_in_release_mode_failed,
+    )
+
+    from lint.files_unchanged import (
+        test_files_unchanged_pass,
+        test_files_unchanged_fail,
+    )
+
 
 #    def test_critical_missingfiles_example(self):
 #        """Tests for missing nextflow config and main.nf files"""

diff --git a/tests/test_utils.py b/tests/test_utils.py
@@ -5,7 +5,10 @@
 import nf_core.create
 import nf_core.utils
 
+import mock
 import os
+import pytest
+import requests
 import tempfile
 import unittest
 
@@ -92,3 +95,32 @@ def test_list_files_no_git(self):
         pipeline_obj = nf_core.utils.Pipeline(tmpdir)
         pipeline_obj._list_files()
         assert tmp_fn in pipeline_obj.files
+
+    def test_pip_package_pass(self):
+        result = nf_core.utils.pip_package("multiqc=1.10")
+        assert type(result) == dict
+
+    @mock.patch("requests.get")
+    def test_pip_package_timeout(self, mock_get):
+        """Tests the PyPi connection and simulates a request timeout, which should
+        return in an addiional warning in the linting"""
+        # Define the behaviour of the request get mock
+        mock_get.side_effect = requests.exceptions.Timeout()
+        # Now do the test
+        with pytest.raises(LookupError):
+            nf_core.utils.pip_package("multiqc=1.10")
+
+    @mock.patch("requests.get")
+    def test_pip_package_connection_error(self, mock_get):
+        """Tests the PyPi connection and simulates a connection error, which should
+        result in an additional warning, as we cannot test if dependent module is latest"""
+        # Define the behaviour of the request get mock
+        mock_get.side_effect = requests.exceptions.ConnectionError()
+        # Now do the test
+        with pytest.raises(LookupError):
+            nf_core.utils.pip_package("multiqc=1.10")
+
+    def test_pip_erroneous_package(self):
+        """ Tests the PyPi API package information query """
+        with pytest.raises(ValueError):
+            nf_core.utils.pip_package("not_a_package=1.0")