adds missing code handling and tests for external tests

Author: BWMac

src/dcqc/tests/bioformats_info_test.py

@@ -4,16 +4,19 @@
 
 class BioFormatsInfoTest(ExternalBaseTest):
     tier = 2
+    pass_code = "0"
     target: SingleTarget
 
     def generate_process(self) -> Process:
         path = self.target.file.stage()
+        string_path = self._short_string_path(path, "dcqc-staged-")
+
         command_args = [
             "/opt/bftools/showinf",
             "-nopix",
             "-novalid",
             "-nocore",
-            path,
+            string_path,
         ]
         process = Process(
             container="quay.io/sagebionetworks/bftools:latest",

src/dcqc/tests/ome_xml_schema_test.py

@@ -4,13 +4,16 @@
 
 class OmeXmlSchemaTest(ExternalBaseTest):
     tier = 2
+    pass_code = "0"
     target: SingleTarget
 
     def generate_process(self) -> Process:
         path = self.target.file.stage()
+        string_path = self._short_string_path(path, "dcqc-staged-")
+
         command_args = [
             "/opt/bftools/xmlvalid",
-            path,
+            string_path,
         ]
         process = Process(
             container="quay.io/sagebionetworks/bftools:latest",

tests/test_tests.py

@@ -126,13 +126,63 @@ def test_that_the_bioformats_info_test_command_is_produced(test_targets):
     assert "showinf" in process.command
 
 
+def test_that_the_bioformats_info_test_correctly_interprets_exit_code_0_and_1(
+    test_files, mocker
+):
+    # 0 is pass, 1 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")
+        pass_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
+        fail_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
+
+        test = tests.BioFormatsInfoTest(target)
+        mocker.patch.object(test, "_find_process_outputs", return_value=pass_outputs)
+        test_status = test.get_status()
+        assert test_status == TestStatus.PASS
+
+        test = tests.BioFormatsInfoTest(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_the_ome_xml_schema_test_command_is_produced(test_targets):
     target = test_targets["tiff"]
     test = tests.OmeXmlSchemaTest(target)
     process = test.generate_process()
     assert "xmlvalid" in process.command
 
 
+def test_that_the_ome_xml_info_test_correctly_interprets_exit_code_0_and_1(
+    test_files, mocker
+):
+    # 0 is pass, 1 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")
+        pass_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
+        fail_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
+
+        test = tests.OmeXmlSchemaTest(target)
+        mocker.patch.object(test, "_find_process_outputs", return_value=pass_outputs)
+        test_status = test.get_status()
+        assert test_status == TestStatus.PASS
+
+        test = tests.OmeXmlSchemaTest(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_the_md5_checksum_test_can_be_retrieved_by_name():
     test = BaseTest.get_subclass_by_name("Md5ChecksumTest")
     assert test is tests.Md5ChecksumTest