fixed tests

flowcraft/tests/template_tests/test_mapping2json.py

@@ -28,7 +28,6 @@
     }
 }
 
-#
 plasmid_length = {
     "ACC1": "10",
     "ACC2": "10"
@@ -43,16 +42,13 @@ def fetch_file(tmpdir, request):
     # 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)
+    return json_dict, str(depth_file)
 
 
 def test_depth_file_reader(tmpdir):
@@ -62,7 +58,7 @@ def test_depth_file_reader(tmpdir):
 
     # create a temporary file to make a dict from
     file_handle = tmpdir.join("test_depth_file.txt")
-    file.write("seq1\t1\t30")
+    file_handle.write("seq1\t1\t30")
 
     # execute the function to get the dict
     result_dict = mapping2json.depth_file_reader(open(str(file)))
@@ -92,22 +88,30 @@ def test_generate_file(fetch_file):
     """
     This function tests if the output json file is generated
     """
-    _, depth_file = fetch_file
+    json_dict, depth_file = fetch_file
+    # executes the function to be tested
+    mapping2json.main(str(depth_file), str(json_dict), "0", "test")
     assert os.path.isfile("{}_mapping.json".format(depth_file))
 
 
 def test_generate_report(fetch_file):
     """
     This tests if the report.json file is generated
     """
+    json_dict, depth_file = fetch_file
+    # executes the function to be tested
+    mapping2json.main(str(depth_file), str(json_dict), "0", "test")
     assert os.path.isfile(".report.json")
 
 
 def test_generated_dict(fetch_file):
     """
     This function checks if the file contains a dict
     """
-    result_dict, _ = fetch_file
+    json_dict, depth_file = fetch_file
+    # 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 isinstance(result_dict, dict)
 
 
@@ -116,5 +120,8 @@ 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}
-    result_dict, _ = fetch_file
+    json_dict, depth_file = fetch_file
+    # 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 result_dict == expected_dict

flowcraft/tests/template_tests/test_mashdist2json.py

@@ -10,44 +10,49 @@ def fetch_file(tmpdir, request):
     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])))
-
     # finalizer statement that removes .report.json
     def remove_test_files():
         os.remove(".report.json")
     request.addfinalizer(remove_test_files)
 
-    return result_dict, str(mash_file)
+    return str(mash_file)
 
 
 def test_generate_file(fetch_file):
     """
     This function tests if the files generated by this template script are
     created
     """
-    _, mash_file = fetch_file
+    mash_file = fetch_file
+    mashdist2json.main(str(mash_file), "0.5", "test", "assembly_file")
     assert os.path.isfile("{}.json".format(mash_file.split(".")[0]))
 
 
 def test_generate_report(fetch_file):
     """
     This tests if the report.json file is generated
     """
+    mash_file = fetch_file
+    mashdist2json.main(str(mash_file), "0.5", "test", "assembly_file")
     assert os.path.isfile(".report.json")
 
 
 def test_generated_dict(fetch_file):
     """
     This function checks if the file contains a dict
     """
-    result_dict, _ = fetch_file
+    mash_file = fetch_file
+    mashdist2json.main(str(mash_file), "0.5", "test", "assembly_file")
+    result_dict = json.load(open("{}.json".format(
+        str(mash_file).split(".")[0])))
     assert isinstance(result_dict, dict)
 
 
 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
+    mash_file = fetch_file
+    mashdist2json.main(str(mash_file), "0.5", "test", "assembly_file")
+    result_dict = json.load(open("{}.json".format(
+        str(mash_file).split(".")[0])))
     assert result_dict == expected_dict

flowcraft/tests/template_tests/test_mashscreen2json.py

@@ -10,44 +10,49 @@ def fetch_file(tmpdir, request):
     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])))
-
     # finalizer statement that removes .report.json
     def remove_test_files():
         os.remove(".report.json")
     request.addfinalizer(remove_test_files)
 
-    return result_dict, str(mash_file)
+    return str(mash_file)
 
 
 def test_generate_file(fetch_file):
     """
     This function tests if the files generated by this template script are
     created
     """
-    _, mash_file = fetch_file
+    mash_file = fetch_file
+    mashscreen2json.main(str(mash_file), "test")
     assert os.path.isfile("{}.json".format(mash_file.split(".")[0]))
 
 
 def test_generate_report(fetch_file):
     """
     This tests if the report.json file is generated
     """
+    mash_file = fetch_file
+    mashscreen2json.main(str(mash_file), "test")
     assert os.path.isfile(".report.json")
 
 
 def test_generated_dict(fetch_file):
     """
     This function checks if the file contains a dict
     """
-    result_dict, _ = fetch_file
+    mash_file = fetch_file
+    mashscreen2json.main(str(mash_file), "test")
+    result_dict = json.load(open("{}.json".format(
+        str(mash_file).split(".")[0])))
     assert isinstance(result_dict, dict)
 
 
 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
+    mash_file = fetch_file
+    mashscreen2json.main(str(mash_file), "test")
+    result_dict = json.load(open("{}.json".format(
+        str(mash_file).split(".")[0])))
     assert result_dict == expected_dict

flowcraft/tests/template_tests/test_pATLAS_consensus_json.py

@@ -14,52 +14,59 @@ def fetch_file(tmpdir, request):
 
     list_of_files = [str(mash_file), str(depth_file)]
 
-    pATLAS_consensus_json.main(list_of_files)
-    result_dict = json.load(open("consensus_file.json"))
-
     # finalizer statement that removes .report.json
     def remove_test_files():
         os.remove(".report.json")
     request.addfinalizer(remove_test_files)
 
-    return result_dict
+    return list_of_files
 
 
 def test_generate_file(fetch_file):
     """
     Check if consensus output file is generated
     """
+    list_of_files = fetch_file
+    pATLAS_consensus_json.main(list_of_files)
     assert os.path.isfile("consensus_file.json")
 
 
 def test_generate_report(fetch_file):
     """
     This tests if the report.json file is generated
     """
+    list_of_files = fetch_file
+    pATLAS_consensus_json.main(list_of_files)
     assert os.path.isfile(".report.json")
 
 
 def test_generated_dict(fetch_file):
     """
     This function checks if the file contains a dict
     """
-    result_dict = fetch_file
+    list_of_files = fetch_file
+    pATLAS_consensus_json.main(list_of_files)
+    result_dict = json.load(open("consensus_file.json"))
     assert isinstance(result_dict, dict)
 
 
 def test_generated_dict_contents1(fetch_file):
     """
     Checks if accession in both expected and result dict is the same
     """
-    result_dict = fetch_file
+    list_of_files = fetch_file
+    pATLAS_consensus_json.main(list_of_files)
+    result_dict = json.load(open("consensus_file.json"))
     assert list(result_dict.keys())[0] == "ACC1"
 
 
 def test_generated_dict_contents2(fetch_file):
     """
     checks if the resulting values for each type of file are the proper type
     """
-    result_dict = fetch_file
+    list_of_files = fetch_file
+    pATLAS_consensus_json.main(list_of_files)
+    result_dict = json.load(open("consensus_file.json"))
     first_file_values = list(result_dict[
                                  list(result_dict.keys())[0]].values())[0]
     second_file_values = list(result_dict[
@@ -74,5 +81,7 @@ def test_generated_dict_contents3(fetch_file):
     """
     checks that the accession in dict must have two keys
     """
-    result_dict = fetch_file
+    list_of_files = fetch_file
+    pATLAS_consensus_json.main(list_of_files)
+    result_dict = json.load(open("consensus_file.json"))
     assert len(list(result_dict[list(result_dict.keys())[0]].keys())) == 2