Merge pull request #47 from Sage-Bionetworks-Workflows/bwmac/orca-268/tiff_date_test

[ORCA-268] Adds TiffDateTimeTest

Author: BWMac

src/dcqc/suites/suites.py

@@ -24,7 +24,7 @@ class TiffSuite(FileSuite):
     file_type = FileType.get_file_type("TIFF")
     add_tests = (
         tests.LibTiffInfoTest,
-        tests.GrepDateTest,
+        tests.TiffDateTimeTest,
         tests.TiffTag306DateTimeTest,
     )
 

src/dcqc/tests/__init__.py

@@ -8,4 +8,5 @@
 from dcqc.tests.md5_checksum_test import Md5ChecksumTest
 from dcqc.tests.ome_xml_schema_test import OmeXmlSchemaTest
 from dcqc.tests.paired_fastq_parity_test import PairedFastqParityTest
+from dcqc.tests.tiff_date_time_test import TiffDateTimeTest
 from dcqc.tests.tiff_tag_306_date_time_test import TiffTag306DateTimeTest

src/dcqc/tests/tiff_date_time_test.py

@@ -0,0 +1,32 @@
+from dcqc.target import SingleTarget
+from dcqc.tests.base_test import ExternalBaseTest, Process
+
+
+class TiffDateTimeTest(ExternalBaseTest):
+    tier = 4
+    pass_code = "1"
+    target: SingleTarget
+
+    def generate_process(self) -> Process:
+        path = self.target.file.stage()
+
+        command_args = [
+            "tifftools",
+            "dump",
+            f"'{path.name}'",
+            "--json",
+            "--silent",
+            "|",
+            "jq",
+            "-e",
+            "'.[].ifds[].tags[]'.data",
+            "|",
+            "grep",
+            "-Ei",
+            "'date|time'",
+        ]
+        process = Process(
+            container="ghcr.io/sage-bionetworks-workflows/tifftools:latest",
+            command_args=command_args,
+        )
+        return process

tests/data/date_tag.tif

@@ -8,9 +8,9 @@
 from dcqc.tests import (
     BaseTest,
     FileExtensionTest,
-    GrepDateTest,
     LibTiffInfoTest,
     TestStatus,
+    TiffDateTimeTest,
     TiffTag306DateTimeTest,
 )
 
@@ -20,7 +20,7 @@
 
 class RedundantFileSuite(TiffSuite):
     file_type = FileType.get_file_type("None")
-    del_tests = (LibTiffInfoTest, GrepDateTest, TiffTag306DateTimeTest)
+    del_tests = (LibTiffInfoTest, TiffDateTimeTest, TiffTag306DateTimeTest)
 
 
 class DummyTest(BaseTest):
@@ -105,7 +105,7 @@ def test_for_an_error_when_building_suite_from_tests_with_diff_targets(test_targ
 def test_that_a_suite_will_consider_non_required_failed_tests(test_targets):
     target = test_targets["bad"]
     required_tests = []
-    skipped_tests = ["LibTiffInfoTest", "GrepDateTest", "TiffTag306DateTimeTest"]
+    skipped_tests = ["LibTiffInfoTest", "TiffDateTimeTest", "TiffTag306DateTimeTest"]
     suite = SuiteABC.from_target(target, required_tests, skipped_tests)
     suite_status = suite.compute_status()
     assert suite_status == SuiteStatus.AMBER
@@ -114,7 +114,7 @@ def test_that_a_suite_will_consider_non_required_failed_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", "GrepDateTest", "TiffTag306DateTimeTest"]
+    skipped_tests = ["LibTiffInfoTest", "TiffDateTimeTest", "TiffTag306DateTimeTest"]
     suite = SuiteABC.from_target(target, required_tests, skipped_tests)
     suite_status = suite.compute_status()
     assert suite_status == SuiteStatus.RED

tests/test_suites.py

@@ -295,6 +295,38 @@ def test_that_the_tifftag306datetimetest_correctly_interprets_exit_code_0_and_1(
         assert test_status == TestStatus.FAIL
 
 
+def test_that_the_tiffdatetimetest_command_is_produced(test_targets):
+    target = test_targets["tiff"]
+    test = tests.TiffDateTimeTest(target)
+    process = test.generate_process()
+    assert "grep" in process.command
+
+
+def test_that_the_tiffdatetimetest_correctly_interprets_exit_code_0_and_1(
+    test_files, mocker
+):
+    # 1 is pass, 0 is fail
+    tiff_file = test_files["tiff"]
+    target = SingleTarget(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")
+        fail_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
+        pass_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
+
+        test = tests.TiffDateTimeTest(target)
+        mocker.patch.object(test, "_find_process_outputs", return_value=pass_outputs)
+        test_status = test.get_status()
+        assert test_status == TestStatus.PASS
+
+        test = tests.TiffDateTimeTest(target)
+        mocker.patch.object(test, "_find_process_outputs", return_value=fail_outputs)
+        test_status = test.get_status()
+        assert test_status == TestStatus.FAIL
+
+
 def test_that_paired_fastq_parity_test_correctly_passes_identical_fastq_files(
     test_files,
 ):