added custom fixtures to plasmid templates tests

flowcraft/tests/template_tests/test_mapping2json.py

@@ -1,5 +1,6 @@
 import os
 import json
+import pytest
 import flowcraft.templates.mapping2json as mapping2json
 
 depth_dict_coverage = {
@@ -34,6 +35,26 @@
 }
 
 
+@pytest.fixture
+def fetch_file(tmpdir, request):
+    # create a temporary file depth txt file
+    depth_file = tmpdir.join("test_depth_file.txt")
+    depth_file.write("ACC1\t1\t30")
+    # creates a temporary file with the json_dict
+    json_dict = tmpdir.join("test_json_dict.json")
+    json_dict.write('{"ACC1": 2000}')
+    # executes the function to be tested
+    mapping2json.main(str(depth_file), str(json_dict), "0", "test")
+    result_dict = json.load(open("{}_mapping.json".format(str(depth_file))))
+
+    # finalizer statement that removes .report.json
+    def remove_test_files():
+        os.remove(".report.json")
+    request.addfinalizer(remove_test_files)
+
+    return result_dict, str(depth_file)
+
+
 def test_depth_file_reader(tmpdir):
     """
     test the output of depth_file_reader_function to be a given dict
@@ -67,78 +88,33 @@ def test_generate_jsons():
     )
 
 
-def test_generate_file(tmpdir):
+def test_generate_file(fetch_file):
     """
-    This function tests if the files are generated by the main function.
-    .report.json and the file to import in pATLAS.
+    This function tests if the output json file is generated
     """
+    _, depth_file = fetch_file
+    assert os.path.isfile("{}_mapping.json".format(depth_file))
 
-    # create a temporary file depth txt file
-    depth_file = tmpdir.join("test_depth_file.txt")
-    depth_file.write("seq1\t1\t30")
-
-    # creates a temporary file with the json_dict
-    json_dict = tmpdir.join("test_json_dict.json")
-    json_dict.write('{"seq1": 2000}')
-
-    # executes the function to be tested
-    mapping2json.main(str(depth_file), str(json_dict), "0", "test")
-
-    assert_message = []
-    # conditions to check that files are generated
-    if not os.path.isfile("{}_mapping.json".format(str(depth_file))):
-        assert_message.append("_mapping.json not created")
-    if not os.path.isfile(".report.json"):
-        assert_message.append(".report.json file was not created")
-
-    # remove the .report.json file
-    os.remove(".report.json")
 
-    assert not assert_message, "errors occurred:\n{}".format(
-        "\n".join(assert_message)
-    )
+def test_generate_report(fetch_file):
+    """
+    This tests if the report.json file is generated
+    """
+    assert os.path.isfile(".report.json")
 
 
-def test_generated_dict(tmpdir):
+def test_generated_dict(fetch_file):
     """
-    This function tests if the files generated by this template script are
-    created
+    This function checks if the file contains a dict
     """
+    result_dict, _ = fetch_file
+    assert isinstance(result_dict, dict)
 
-    # create a temporary file depth txt file
-    depth_file = tmpdir.join("test_depth_file.txt")
-    depth_file.write("ACC1\t1\t30")
-
-    # creates a temporary file with the json_dict
-    json_dict = tmpdir.join("test_json_dict.json")
-    json_dict.write('{"ACC1": 2000}')
 
+def test_generated_dict_contents(fetch_file):
+    """
+    This function tests if the dictionary in the file has the required fields
+    """
     expected_dict = {"ACC1": 0.0}
-
-    # executes the function to be tested
-    mapping2json.main(str(depth_file), str(json_dict), "0", "test")
-
-    result_dict = json.load(open("{}_mapping.json".format(str(depth_file))))
-
-    assert_message = []
-
-    # checks if result_dict is indeed a dictionary
-    if not isinstance(result_dict, dict):
-        assert_message.append("Contents of the generated file must be a "
-                              "dictionary.")
-
-    if not result_dict == expected_dict:
-        assert_message.append("The expected dictionary must be equal to the "
-                              "one present in the generated file.\n"
-                              "Expected: {}\n"
-                              "Result: {}". format(
-            json.dumps(expected_dict),
-            json.dumps(result_dict)
-        ))
-
-    # remove the .report.json file
-    os.remove(".report.json")
-
-    assert not assert_message, "Errors occurred:\n{}".format(
-        "\n".join(assert_message)
-    )
+    result_dict, _ = fetch_file
+    assert result_dict == expected_dict

flowcraft/tests/template_tests/test_mashdist2json.py

@@ -1,73 +1,53 @@
 import os
 import json
+import pytest
 import flowcraft.templates.mashdist2json as mashdist2json
 
 
-def test_generate_file(tmpdir):
-    """
-    This function tests if the files generated by this template script are
-    created
-    """
-
+@pytest.fixture
+def fetch_file(tmpdir, request):
     # create a temporary file mash screen txt file
     mash_file = tmpdir.join("test_depth_file.txt")
     mash_file.write("ACC1\tseq1\t0\t900/1000")
 
     mashdist2json.main(str(mash_file), "0.5", "test", "assembly_file")
+    result_dict = json.load(open("{}.json".format(
+            str(mash_file).split(".")[0])))
 
-    assert_message = []
-    # conditions to check that files are generated
-    if not os.path.isfile("{}.json".format(
-            str(mash_file).split(".")[0])):
-        assert_message.append("mash dist json not created")
-    if not os.path.isfile(".report.json"):
-        assert_message.append(".report.json file was not created")
-
-    # remove the .report.json file
-    os.remove(".report.json")
+    # finalizer statement that removes .report.json
+    def remove_test_files():
+        os.remove(".report.json")
+    request.addfinalizer(remove_test_files)
 
-    assert not assert_message, "errors occurred:\n{}".format(
-        "\n".join(assert_message)
-    )
+    return result_dict, str(mash_file)
 
 
-def test_generated_dict(tmpdir):
+def test_generate_file(fetch_file):
     """
     This function tests if the files generated by this template script are
     created
     """
+    _, mash_file = fetch_file
+    assert os.path.isfile("{}.json".format(mash_file.split(".")[0]))
 
-    # create a temporary file mash screen txt file
-    mash_file = tmpdir.join("test_depth_file.txt")
-    mash_file.write("ACC1\tseq1\t0\t900/1000")
 
-    # the expected result from loading the dictionary in the generated file
-    expected_dict = {"ACC1": [1.0, 0.9, "seq1"]}
-
-    mashdist2json.main(str(mash_file), "0.5", "test", "assembly_file")
-
-    result_dict = json.load(open("{}.json".format(
-            str(mash_file).split(".")[0])))
-
-    assert_message = []
+def test_generate_report(fetch_file):
+    """
+    This tests if the report.json file is generated
+    """
+    assert os.path.isfile(".report.json")
 
-    # checks if result_dict is indeed a dictionary
-    if not isinstance(result_dict, dict):
-        assert_message.append("Contents of the generated file must be a "
-                              "dictionary.")
 
-    if not result_dict == expected_dict:
-        assert_message.append("The expected dictionary must be equal to the "
-                              "one present in the generated file.\n"
-                              "Expected: {}\n"
-                              "Result: {}". format(
-            json.dumps(expected_dict),
-            json.dumps(result_dict)
-        ))
+def test_generated_dict(fetch_file):
+    """
+    This function checks if the file contains a dict
+    """
+    result_dict, _ = fetch_file
+    assert isinstance(result_dict, dict)
 
-    # remove the .report.json file
-    os.remove(".report.json")
 
-    assert not assert_message, "Errors occurred:\n{}".format(
-        "\n".join(assert_message)
-    )
+def test_generated_dict_contents(fetch_file):
+    # the expected result from loading the dictionary in the generated file
+    expected_dict = {"ACC1": [1.0, 0.9, "seq1"]}
+    result_dict, _ = fetch_file
+    assert result_dict == expected_dict

flowcraft/tests/template_tests/test_mashscreen2json.py

@@ -1,74 +1,53 @@
 import os
 import json
+import pytest
 import flowcraft.templates.mashscreen2json as mashscreen2json
 
 
-def test_generate_file(tmpdir):
-    """
-    This function tests if the files generated by this template script are
-    created
-    """
-
+@pytest.fixture
+def fetch_file(tmpdir, request):
     # create a temporary file mash screen txt file
     mash_file = tmpdir.join("test_depth_file.txt")
     mash_file.write("100\tNA\t30\tNA\tACC1")
 
     mashscreen2json.main(str(mash_file), "test")
+    result_dict = json.load(open("{}.json".format(
+        str(mash_file).split(".")[0])))
 
-    assert_message = []
-    # conditions to check that files are generated
-    if not os.path.isfile("{}.json".format(
-            str(mash_file).split(".")[0])):
-        assert_message.append("mash screen json not created")
-    if not os.path.isfile(".report.json"):
-        assert_message.append(".report.json file was not created")
-
-    # remove the .report.json file
-    os.remove(".report.json")
+    # finalizer statement that removes .report.json
+    def remove_test_files():
+        os.remove(".report.json")
+    request.addfinalizer(remove_test_files)
 
-    assert not assert_message, "errors occurred:\n{}".format(
-        "\n".join(assert_message)
-    )
+    return result_dict, str(mash_file)
 
 
-def test_generated_dict(tmpdir):
+def test_generate_file(fetch_file):
     """
     This function tests if the files generated by this template script are
     created
     """
+    _, mash_file = fetch_file
+    assert os.path.isfile("{}.json".format(mash_file.split(".")[0]))
 
-    # create a temporary file mash screen txt file
-    mash_file = tmpdir.join("test_depth_file.txt")
-    mash_file.write("100\tNA\t30\tNA\tACC1")
-
-    # the expected result from loading the dictionary in the generated file
-    expected_dict = {"ACC1": [100.0, 1]}
-
-    mashscreen2json.main(str(mash_file), "test")
-
-    result_dict = json.load(open("{}.json".format(
-            str(mash_file).split(".")[0])))
-
-    assert_message = []
 
-    # checks if result_dict is indeed a dictionary
-    if not isinstance(result_dict, dict):
-        assert_message.append("Contents of the generated file must be a "
-                              "dictionary.")
+def test_generate_report(fetch_file):
+    """
+    This tests if the report.json file is generated
+    """
+    assert os.path.isfile(".report.json")
 
-    if not result_dict == expected_dict:
-        assert_message.append("The expected dictionary must be equal to the "
-                              "one present in the generated file.\n"
-                              "Expected: {}\n"
-                              "Result: {}". format(
-            json.dumps(expected_dict),
-            json.dumps(result_dict)
-        ))
 
-    # remove the .report.json file
-    os.remove(".report.json")
+def test_generated_dict(fetch_file):
+    """
+    This function checks if the file contains a dict
+    """
+    result_dict, _ = fetch_file
+    assert isinstance(result_dict, dict)
 
-    assert not assert_message, "Errors occurred:\n{}".format(
-        "\n".join(assert_message)
-    )
 
+def test_generated_dict_contents(fetch_file):
+    # the expected result from loading the dictionary in the generated file
+    expected_dict = {"ACC1": [100.0, 1]}
+    result_dict, _ = fetch_file
+    assert result_dict == expected_dict