run pass new test

scripts/run_tests_within_container.sh

@@ -5,7 +5,7 @@ export KB_AUTH_TOKEN=`cat /kb/module/work/token`
 export PYTHONPATH=$script_dir/../lib:$PATH:$PYTHONPATH
 
 # Set TEST_PATH to run a specific test. Eg: TEST_PATH=test.core.update_taxon_assignments_test
-export TEST_PATH=.
+export TEST_PATH=test.problematic_tests.impl_test
 
 cd $script_dir/../test
 python -m nose --with-coverage --cover-package=GenomeFileUtil --cover-html --cover-html-dir=/kb/module/work/test_coverage --cover-xml --cover-xml-file=/kb/module/work/test_coverage/coverage.xml --nocapture --nologcapture $TEST_PATH

test/problematic_tests/impl_test.py

@@ -0,0 +1,58 @@
+import os
+import pytest
+import traceback
+import unittest
+
+from configparser import ConfigParser
+
+from GenomeFileUtil.GenomeFileUtilImpl import GenomeFileUtil
+
+
+def assert_exception_correct(got: Exception, expected: Exception):
+    """
+    Compare raised exception with expected exception.
+
+    Args:
+        got (Exception): Exception received
+        expected (Exception): Exception expected
+    """
+    err = "".join(traceback.TracebackException.from_exception(got).format())
+    assert got.args == expected.args, err
+    assert type(got) == type(expected)
+
+
+class ImplTest(unittest.TestCase):
+    def setUp(self):
+        config_file = os.environ["KB_DEPLOYMENT_CONFIG"]
+        token = os.environ.get("KB_AUTH_TOKEN", None)
+
+        self.cfg = {}
+        config = ConfigParser()
+        config.read(config_file)
+        for nameval in config.items("GenomeFileUtil"):
+            self.cfg[nameval[0]] = nameval[1]
+        self.cfg["KB_AUTH_TOKEN"] = token
+
+    def test_invalid_catalog_param_type(self):
+        MAX_THREADS = "MAX_THREADS"
+        THREADS_PER_CPU = "THREADS_PER_CPU"
+
+        # max_threads type check fails
+        os.environ["KBASE_SECURE_CONFIG_PARAM_MAX_THREADS"] = "10.5"
+        os.environ["KBASE_SECURE_CONFIG_PARAM_THREADS_PER_CPU"] = "2.5"
+
+        with pytest.raises(Exception) as got:
+            GenomeFileUtil(self.cfg)
+        assert_exception_correct(
+            got.value, ValueError(f"{MAX_THREADS} must be of type {int.__name__}")
+        )
+
+        # threads_per_cpu type check fails
+        os.environ["KBASE_SECURE_CONFIG_PARAM_MAX_THREADS"] = "10"
+        os.environ["KBASE_SECURE_CONFIG_PARAM_THREADS_PER_CPU"] = "2.8e"
+
+        with pytest.raises(Exception) as got:
+            GenomeFileUtil(self.cfg)
+        assert_exception_correct(
+            got.value, ValueError(f"{THREADS_PER_CPU} must be of type {float.__name__}")
+        )

test/problematic_tests/save_genome_test.py

@@ -5,7 +5,6 @@
 import os  # noqa: F401
 import shutil
 import time
-import traceback
 import unittest
 import urllib.error
 import urllib.parse
@@ -14,7 +13,6 @@
 from os import environ
 
 import requests  # noqa: F401
-from pytest import raises
 
 from installed_clients.AssemblyUtilClient import AssemblyUtil
 from installed_clients.DataFileUtilClient import DataFileUtil
@@ -26,19 +24,6 @@
 from installed_clients.WorkspaceClient import Workspace as workspaceService
 
 
-def assert_exception_correct(got: Exception, expected: Exception):
-    """
-    Compare raised exception with expected exception.
-
-    Args:
-        got (Exception): Exception received
-        expected (Exception): Exception expected
-    """
-    err = "".join(traceback.TracebackException.from_exception(got).format())
-    assert got.args == expected.args, err
-    assert type(got) == type(expected)
-
-
 class SaveGenomeTest(unittest.TestCase):
 
     @classmethod
@@ -153,9 +138,6 @@ def getImpl(self):
     def getContext(self):
         return self.__class__.ctx
 
-    def getCfg(self):
-        return self.__class__.cfg
-
     def start_test(self):
         testname = inspect.stack()[1][3]
         print(('\n*** starting test: ' + testname + ' **'))
@@ -210,34 +192,6 @@ def test_one_genome_with_hidden(self):
         ret = self.getImpl().save_one_genome(self.ctx, params)[0]
         self.check_save_one_genome_output(ret, genome_name)
 
-    def test_invalid_catalog_param_type(self):
-        self.start_test()
-
-        MAX_THREADS = "MAX_THREADS"
-        THREADS_PER_CPU = "THREADS_PER_CPU"
-
-        # max_threads type check fails
-        os.environ["KBASE_SECURE_CONFIG_PARAM_MAX_THREADS"] = "10.5"
-        os.environ["KBASE_SECURE_CONFIG_PARAM_THREADS_PER_CPU"] = "2.5"
-
-        with raises(Exception) as got:
-            GenomeFileUtil(self.getCfg())
-        assert_exception_correct(
-            got.value,
-            ValueError(f"{MAX_THREADS} must be of type {int.__name__}")
-        )
-
-        # threads_per_cpu type check fails
-        os.environ["KBASE_SECURE_CONFIG_PARAM_MAX_THREADS"] = "10"
-        os.environ["KBASE_SECURE_CONFIG_PARAM_THREADS_PER_CPU"] = "2.8e"
-
-        with raises(Exception) as got:
-            GenomeFileUtil(self.getCfg())
-        assert_exception_correct(
-            got.value,
-            ValueError(f"{THREADS_PER_CPU} must be of type {float.__name__}")
-        )
-
     def test_GenomeInterface_check_dna_sequence_in_features(self):
         # no feature in genome
         genome = {'missing_features': 'features'}