changed docker image to one in GHCR

Author: andrewelamb

src/dcqc/tests/h5ad_htan_validator_test.py

@@ -9,8 +9,8 @@ class H5adHtanValidatorTest(ExternalBaseTest):
     """
 
     tier = TestTier.INTERNAL_CONFORMANCE
-    pass_code = 1
-    fail_code = 0
+    pass_code = 0
+    fail_code = 1
     failure_reason_location = "std_out"
     target: SingleTarget
 
@@ -22,7 +22,7 @@ def generate_process(self) -> Process:
             f"'{path.name}'",
         ]
         process = Process(
-            container="h5ad:latest",
+            container="ghcr.io/sage-bionetworks-workflows/htan-h5ad-validator:0.1",
             command_args=command_args,
         )
         return process

tests/test_external_tests.py

@@ -446,27 +446,65 @@ def setup_method(self, test_targets):
         self.good_h5ad_test = tests.H5adHtanValidatorTest(self.good_h5ad_target)
         self.bad_h5ad_target = test_targets["htan_bad_h5ad"]
         self.bad_h5ad_test = tests.H5adHtanValidatorTest(self.bad_h5ad_target)
+        self.txt_target = test_targets["good_txt"]
+        self.txt_test = tests.H5adHtanValidatorTest(self.txt_target)
 
     def test_that_the_command_is_produced(self):
         process = self.good_h5ad_test.generate_process()
         assert "/usr/local/bin/h5ad.py" in process.command
 
     @docker_enabled_test
-    def test_that_the_exit_code_is_0_when_it_should_be(self):
+    def test_that_the_exit_code_is_1_when_it_should_be(self):
         process = self.bad_h5ad_test.generate_process()
         executor = DockerExecutor(
             process.container, process.command, self.bad_h5ad_target.file.url
         )
         executor.execute()
-        assert executor.exit_code == "0"
+        assert executor.std_out == (
+            "HTAN h5ad File Validator\n"
+            "File:  htan_bad.h5ad\n"
+            "Running cellxgene-schema\n"
+            "Cellxgene run has errors. Please note errors or warnings in the output file.\n"
+            "Running HTAN-specific validation\n"
+            "HTAN Validation Failed.\n"
+            "Please check output file for errors.\n"
+            "\n"
+        )
+        assert executor.exit_code == "1"
 
     @docker_enabled_test
-    def test_that_the_exit_code_is_1_when_it_should_be(self):
+    def test_that_the_exit_code_is_0_when_it_should_be(self):
         process = self.good_h5ad_test.generate_process()
         executor = DockerExecutor(
             process.container, process.command, self.good_h5ad_target.file.url
         )
         executor.execute()
+        assert executor.std_out == (
+            "HTAN h5ad File Validator\n"
+            "File:  htan_good.h5ad\n"
+            "Running cellxgene-schema\n"
+            "Cellxgene run successful. Please check the output file to see if warnings exist.\n"
+            "Running HTAN-specific validation\n"
+            "Validation Passed!\n"
+            "\n"
+        )
+        assert executor.exit_code == "0"
+
+    @docker_enabled_test
+    def test_that_wrong_file_type_has_1_exit_code(self):
+        process = self.txt_test.generate_process()
+        executor = DockerExecutor(
+            process.container, process.command, self.txt_target.file.url
+        )
+        executor.execute()
+        print(executor.std_out)
+        assert executor.std_out == (
+            "HTAN h5ad File Validator\n"
+            "File:  test.txt\n"
+            "An error occurred while trying to open test.txt\n"
+            "Unable to synchronously open file (file signature not found)\n"
+            "\n"
+        )
         assert executor.exit_code == "1"
 
     def test_that_the_test_correctly_interprets_exit_code_0_and_1(