added sample test for the generated files

Author: tiagofilipe12

flowcraft/templates/pATLAS_consensus_json.py

@@ -83,7 +83,6 @@ def main(list_of_jsons):
 
     json_dic = {
         "patlas_mashscreen": json_dict
-        # TODO add information for report webapp
     }
 
     with open(".report.json", "w") as json_report:

flowcraft/tests/template_tests/test_pATLAS_consensus_json.py

@@ -1,4 +1,6 @@
 import os
+import re
+import json
 import flowcraft.templates.pATLAS_consensus_json as pATLAS_consensus_json
 
 
@@ -33,3 +35,74 @@ def test_generate_file(tmpdir):
     assert not assert_message, "errors occurred:\n{}".format(
         "\n".join(assert_message)
     )
+
+
+def test_generated_dict(tmpdir):
+    """
+    Test the dictionary generated by the script. However, since the dict is
+    only outputted to a file it is needed that we read the generated file
+    in order to check the result.
+    """
+
+    # create a temporary file mash screen txt file
+    mash_file = tmpdir.join("mash_file.txt")
+    depth_file = tmpdir.join("test_depth_file.txt")
+    mash_file.write('{"ACC1": ["0.9", "1"]}')
+    depth_file.write('{"ACC1": 0.9}')
+
+    list_of_files = [str(mash_file), str(depth_file)]
+
+    # the expected result from loading the dictionary in the generated file
+    expected_dict = {"ACC1":
+                         {"/tmp/pytest-of-tiago/pytest-1/test_generated_dict0/"
+                          "mash_file.txt": ["0.9", "1"],
+                          "/tmp/pytest-of-tiago/pytest-1/test_generated_dict0/"
+                          "test_depth_file.txt": 0.9}
+                     }
+
+    pATLAS_consensus_json.main(list_of_files)
+
+    result_dict = json.load(open("consensus_file.json"))
+
+    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.")
+
+    # checks if the accession key matches between the expected result and the
+    # actual result
+    if not list(result_dict.keys())[0] == list(expected_dict.keys())[0]:
+        assert_message.append("Expected key doesn't match the resulting key "
+                              "in dict from file.\nExpected value: {}\n"
+                              "Result value: {}".format(
+            list(expected_dict.keys())[0],
+            list(result_dict.keys())[0]
+        ))
+
+    # checks that the accession must have two keys
+    if not len(list(result_dict[list(result_dict.keys())[0]].keys())) == 2:
+        assert_message.append("This dictionary must contain only two keys"
+                              "per accession number. It had ".format(
+            len(list(result_dict[list(result_dict.keys())[0]].keys()))
+        ))
+
+    # checks if the resulting values for each type of file are the proper type:
+    first_file_values = list(result_dict[
+                                 list(result_dict.keys())[0]].values())[0]
+    second_file_values = list(result_dict[
+                                 list(result_dict.keys())[0]].values())[1]
+    list_of_checks = [isinstance(first_file_values, list),
+                      isinstance(second_file_values, float)]
+    if not all(list_of_checks):
+        assert_message.append("Value of the 1 element in each accession "
+                              "dictionary must be a list and the 2 element"
+                              " must be a str.\nOffending value: {} "
+                              "element".format(" ".join(
+            [str(x + 1) for x, el in enumerate(list_of_checks) if not el]
+        )))
+
+    assert not assert_message, "Errors occurred:\n{}".format(
+        "\n".join(assert_message)
+    )