Merge pull request #26 from Sage-Bionetworks-Workflows/ataylor/ORCA-136/grep-date-test

[ORCA-136] Add rudimental PHI detection by doing a grep

Author: thomasyu888

src/dcqc/suites/suites.py

@@ -22,7 +22,7 @@ class JsonLdSuite(JsonSuite):
 
 class TiffSuite(FileSuite):
     file_type = FileType.get_file_type("TIFF")
-    add_tests = (tests.LibTiffInfoTest,)
+    add_tests = (tests.LibTiffInfoTest, tests.GrepDateTest)
 
 
 class OmeTiffSuite(TiffSuite):

src/dcqc/tests/tests.py

@@ -136,3 +136,24 @@ def generate_process(self) -> Process:
             command_args=command_args,
         )
         return process
+
+
+class GrepDateTest(ExternalTestMixin, TestABC):
+    tier = 4
+
+    def generate_process(self) -> Process:
+        file = self.get_file()
+        path = file.local_path.as_posix()
+        command_args = [
+            "grep",
+            "-E",
+            "-w",
+            "-i",
+            "'date|time'",
+            path,
+        ]
+        process = Process(
+            container="quay.io/biocontainers/coreutils:8.30--h14c3975_1000",
+            command_args=command_args,
+        )
+        return process

tests/data/test_contains_word_date.txt

@@ -0,0 +1 @@
+This file contains the word date and therefore should fail the GrepDateTest test.

tests/test_suites.py

@@ -4,15 +4,18 @@
 from dcqc.suites.suite_abc import SuiteABC
 from dcqc.suites.suites import FileSuite, OmeTiffSuite, TiffSuite
 from dcqc.tests.test_abc import TestABC, TestStatus
-from dcqc.tests.tests import FileExtensionTest, LibTiffInfoTest
+from dcqc.tests.tests import FileExtensionTest, GrepDateTest, LibTiffInfoTest
 
 FileType("None", ())
 FileType("Unpaired", ())
 
 
 class RedundantFileSuite(TiffSuite):
     file_type = FileType.get_file_type("None")
-    del_tests = (LibTiffInfoTest,)
+    del_tests = (
+        LibTiffInfoTest,
+        GrepDateTest,
+    )
 
 
 class DummyTest(TestABC):
@@ -70,7 +73,7 @@ def test_that_the_generic_file_suite_is_retrieved_for_an_unpaired_file_type():
 
 
 def test_that_the_default_required_tests_are_only_tiers_1_and_2(test_suites):
-    suite = test_suites["tiff"]
+    suite = test_suites["jsonld"]
     assert all(test.tier <= 2 for test in suite.tests)
 
 
@@ -97,7 +100,7 @@ def test_for_an_error_when_building_suite_from_tests_with_diff_targets(test_targ
 def test_that_a_suite_will_not_consider_unrequired_tests(test_targets):
     target = test_targets["bad"]
     required_tests = []
-    skipped_tests = ["LibTiffInfoTest"]
+    skipped_tests = ["LibTiffInfoTest", "GrepDateTest"]
     suite = SuiteABC.from_target(target, required_tests, skipped_tests)
     suite_status = suite.compute_status()
     assert suite_status == TestStatus.PASS
@@ -106,7 +109,7 @@ def test_that_a_suite_will_not_consider_unrequired_tests(test_targets):
 def test_that_a_suite_will_consider_required_tests_when_failing(test_targets):
     target = test_targets["bad"]
     required_tests = ["FileExtensionTest"]
-    skipped_tests = ["LibTiffInfoTest"]
+    skipped_tests = ["LibTiffInfoTest", "GrepDateTest"]
     suite = SuiteABC.from_target(target, required_tests, skipped_tests)
     suite_status = suite.compute_status()
     assert suite_status == TestStatus.FAIL

tests/test_tests.py

@@ -192,6 +192,37 @@ def test_that_a_process_can_be_serialized_and_deserialized():
     assert process_dict == process_from_dict.to_dict()
 
 
+def test_that_the_grep_date_test_correctly_interprets_exit_code_0_and_1(
+    test_files, mocker
+):
+    tiff_file = test_files["tiff"]
+    target = Target(tiff_file)
+    with TemporaryDirectory() as tmp_dir:
+        path_0 = Path(tmp_dir, "code_0.txt")
+        path_1 = Path(tmp_dir, "code_1.txt")
+        path_0.write_text("0")
+        path_1.write_text("1")
+        good_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
+        bad_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
+
+        test = tests.GrepDateTest(target)
+        mocker.patch.object(test, "_find_process_outputs", return_value=good_outputs)
+        test_status = test.get_status()
+        assert test_status == TestStatus.PASS
+
+        test = tests.LibTiffInfoTest(target)
+        mocker.patch.object(test, "_find_process_outputs", return_value=bad_outputs)
+        test_status = test.get_status()
+        assert test_status == TestStatus.FAIL
+
+
+def test_that_the_grep_date_test_command_is_produced(test_targets):
+    target = test_targets["tiff"]
+    test = tests.GrepDateTest(target)
+    process = test.generate_process()
+    assert "grep" in process.command
+
+
 def test_for_an_error_when_getting_one_file_from_multi_file_target(test_files):
     file = test_files["good"]
     target = Target(file, file)