Encapsulate NFTestAssert class, rewrite tests

[nwiltsie]

Description

This PR rewrites most of the internals of NFTestAssert in a way that is (mostly) invisible to the outside world. This is the key interface change:

@@ -109,12 +108,9 @@ class NFTestCase:
             self._logger.error(" [ failed ]")
             return False

-        for ass in self.asserts:
+        for assertion in self.asserts:
             try:
-                ass.identify_assertion_files()
-                ass.assert_exists()
-                ass.assert_updated()
-                ass.assert_expected()
+                assertion.perform_assertions()
             except Exception as error:
                 self._logger.error(error.args)
                 self._logger.error(" [ failed ]")

The new perform_assertions() method hides all of the details of identify_assertion_files(), assert_exists(), assert_updated(), and assert_expected(). Decoupling the interface from the implementation details like that makes it easier to test and maintain this code.

In that spirit, I've also re-written all of the tests to test the functionality of the class rather than the implementation details. There are a variety of test fixtures that create an NFTestAssert instance pointing to reference and updated files in a temporary directory. The fixtures are parameterized to test the following situations:

• Usage of a custom script
• The actual file was/wasn't updated after the NFTestAssert was created
• There are 0, 1, or 2 files matching the actual glob
• There are 0, 1, or 2 files matching the expect glob
• The actual and expect files do/don't have the same content

Those parameters are matched with appropriate xfail marks to confirm that the tests do/don't pass in the expected situations. (Aside: by default xfail has strict=False, meaning that tests that unexpectedly pass do not raise errors. That is bonkers.)

Checklist

• This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
  Disclosing PHI is a major problem¹ - Even a small leak can be costly².

• This PR does NOT contain germline genetic data³, RNA-Seq, DNA methylation, microbiome or other molecular data⁴.

• This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have set up or verified the main branch protection rule following the github standards before opening this pull request.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Footnotes

1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩

2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩

3. Genetic information is considered PHI.
   Forensic assays can identify patients with as few as 21 SNPs ↩

4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩

[nwiltsie]

Argh, that's what I get for only running my new tests.

[nwiltsie]

Hmm, I'm not sure why this isn't working in the cloud - it works perfectly for me locally:

$ pytest
======================================== test session starts ========================================
platform darwin -- Python 3.11.4, pytest-7.4.0, pluggy-1.0.0
rootdir: /Users/nwiltsie/src/tool-NFTest
collected 162 items

test/unit/test_NFTestAssert.py xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx [ 38%]
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx            [ 88%]
test/unit/test_NFTestCase.py ..                                                               [ 90%]
test/unit/test_NFTestEnv.py ..                                                                [ 91%]
test/unit/test_NFTestRunner.py .                                                              [ 91%]
test/unit/test_common.py .........                                                            [ 97%]
test/unit/test_syslog.py ....                                                                 [100%]

================================== 22 passed, 140 xfailed in 1.96s ==================================

[nwiltsie]

Well, that's irritating. These log lines from this test from 4e71965 show that the filetimes are all wonky in GitHub Actions:

DEBUG    NFTest:NFTestAssert.py:44 Actual path `/tmp/pytest-of-runner/pytest-0/test_nftest_assert_True_md5_1_11/*.actual` resolved to `/tmp/pytest-of-runner/pytest-0/test_nftest_assert_True_md5_1_11/0.actual`
DEBUG    NFTest:NFTestAssert.py:48 Expected path `/tmp/pytest-of-runner/pytest-0/test_nftest_assert_True_md5_1_11/*.expect` resolved to `/tmp/pytest-of-runner/pytest-0/test_nftest_assert_True_md5_1_11/0.expect`
DEBUG    NFTest:NFTestAssert.py:57 Test creation time: 2024-06-24 23:30:14.720138+00:00
DEBUG    NFTest:NFTestAssert.py:58 Actual mod time:    2024-06-24 23:30:14.716686+00:00

The only fix I can find is to insert time.sleep(0.01) calls in the cases the file needs to be updated, even in the case where the file is explicitly created after the NFTestAssert.

[nwiltsie]

Clearly there's something else going on under the hood. I'll dig in and try again later.