Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/planemo/test/results.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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-1:000000000000 0:26e78fe6e8c4
1 """Describes results.
2
3 Is a JSON.
4 """
5 import json
6 import os
7
8 from planemo.io import error
9
10
11 class StructuredData(object):
12 """Abstraction around a simple data structure describing test results."""
13
14 def __init__(self, json_path=None, data=None):
15 """Create a :class:`StructuredData` from a JSON file."""
16 def data_error():
17 error("An invalid JSON for structured test result data - "
18 "summary information and planemo reports will be "
19 "incorrect.")
20
21 self.json_path = json_path
22 structured_data = {}
23 structured_data_tests = {}
24 if json_path and os.path.exists(json_path) and data is None:
25 try:
26 with open(json_path, "r") as output_json_f:
27 data = json.load(output_json_f)
28 except Exception:
29 data_error()
30 try:
31 structured_data = data
32 structured_data_tests = structured_data["tests"]
33 except Exception:
34 data_error()
35
36 self.structured_data = structured_data
37 self.structured_data_tests = structured_data_tests
38 structured_data_by_id = {}
39 for test in self.structured_data_tests:
40 structured_data_by_id[test["id"]] = test["data"]
41 self.structured_data_by_id = structured_data_by_id
42 self.has_details = "summary" in structured_data
43 if self.has_details:
44 self.read_summary()
45
46 def update(self):
47 """Write out an updated version of this data structure to supplied json path."""
48 with open(self.json_path, "w") as out_f:
49 json.dump(self.structured_data, out_f)
50
51 def set_exit_code(self, exit_code):
52 """Set the exit_code for the this test."""
53 self.structured_data["exit_code"] = exit_code
54
55 def calculate_summary_data_if_needed(self):
56 if "summary" not in self.structured_data:
57 self.calculate_summary_data()
58
59 def calculate_summary_data(self):
60 """Use full details on individual test data to update structured data with summary info."""
61 num_tests = 0
62 num_failures = 0
63 num_skips = 0
64 num_errors = 0
65
66 for test in self.structured_data_tests:
67 test_data = get_dict_value("data", test)
68 status = get_dict_value("status", test_data)
69 num_tests += 1
70 if status == "skip":
71 num_skips += 1
72 elif status == "failure":
73 num_failures += 1
74 elif status == "error":
75 num_errors += 1
76 elif status != "success":
77 raise Exception("Unknown test status encountered [%s]" % status)
78
79 summary = {}
80 summary["num_tests"] = num_tests
81 summary["num_failures"] = num_failures
82 summary["num_skips"] = num_skips
83 summary["num_errors"] = num_errors
84 self.structured_data["summary"] = summary
85 self.read_summary()
86
87 def read_summary(self):
88 """Read summary data into properties on this class."""
89 summary = self.structured_data["summary"]
90 num_tests = summary["num_tests"]
91 num_failures = summary["num_failures"]
92 num_skips = summary["num_skips"]
93 num_errors = summary["num_errors"]
94
95 self.num_tests = num_tests
96 self.num_problems = num_skips + num_errors + num_failures
97
98 self.exit_code = self.structured_data.get("exit_code", None)
99
100 @property
101 def failed_ids(self):
102 """Find set of IDs for failed tests."""
103 ids = set([])
104 for test_data in self.structured_data_tests:
105 if test_data["data"]["status"] == "success":
106 continue
107 test_case = test_data["id"].replace(".test_toolbox.", ".test_toolbox:")
108 ids.add(test_case)
109 return ids
110
111
112 def get_dict_value(key, data):
113 """Return data[key] with improved KeyError."""
114 try:
115 return data[key]
116 except (KeyError, TypeError):
117 raise KeyError("No key [%s] in [%s]" % (key, data))
118
119
120 __all__ = (
121 "StructuredData",
122 "get_dict_value",
123 )