Rerun 551481e

Dockerfile

@@ -5,7 +5,8 @@ MAINTAINER KBase Developer
 RUN pip install --upgrade --extra-index-url=https://pypi.anaconda.org/kbase/simple \
   pip \
   biopython==1.70 \
-  releng-client==0.0.1
+  releng-client==0.0.1 \
+  pytest==7.0.1
 
 COPY ./ /kb/module
 RUN mkdir -p /kb/module/work

lib/GenomeFileUtil/GenomeFileUtilImpl.py

@@ -10,7 +10,11 @@
 from GenomeFileUtil.core.FastaGFFToGenome import FastaGFFToGenome
 from GenomeFileUtil.core.GenbankToGenome import GenbankToGenome
 from GenomeFileUtil.core.GenomeFeaturesToFasta import GenomeFeaturesToFasta
-from GenomeFileUtil.core.GenomeInterface import GenomeInterface
+from GenomeFileUtil.core.GenomeInterface import (
+    GenomeInterface,
+    MAX_THREADS_DEFAULT,
+    THREADS_PER_CPU_DEFAULT,
+)
 from GenomeFileUtil.core.GenomeToGFF import GenomeToGFF
 from GenomeFileUtil.core.GenomeToGenbank import GenomeToGenbank
 from installed_clients.AssemblyUtilClient import AssemblyUtil
@@ -32,6 +36,18 @@ def __init__(self, config):
         self.re_api_url = config['re-api-url']
         self.raw = config
 
+
+def _validate_catalog_param_type(threads_count, var_name, default_val, expected_type):
+    """Helper function to validate catalog params type"""
+    if threads_count is None:
+        print(f"Cannot retrieve {var_name} from the catalog, set {var_name}={default_val}")
+        return default_val
+    print(f"Successfully retrieved {var_name} from the catalog!")
+    try:
+        threads_count = expected_type(threads_count)
+    except ValueError as e:
+        raise ValueError(f"{var_name} must be of type {expected_type.__name__}") from e
+    return threads_count
 #END_HEADER
 
 
@@ -64,6 +80,15 @@ def __init__(self, config):
         self.cfg = SDKConfig(config)
         logging.basicConfig(format='%(created)s %(levelname)s: %(message)s',
                             level=logging.INFO)
+
+        max_threads = os.environ.get("KBASE_SECURE_CONFIG_PARAM_MAX_THREADS")
+        threads_per_cpu = os.environ.get("KBASE_SECURE_CONFIG_PARAM_THREADS_PER_CPU")
+        self.max_threads = _validate_catalog_param_type(
+            max_threads, "MAX_THREADS", MAX_THREADS_DEFAULT, int
+        )
+        self.threads_per_cpu = _validate_catalog_param_type(
+            threads_per_cpu, "THREADS_PER_CPU", THREADS_PER_CPU_DEFAULT, float
+        )
         #END_CONSTRUCTOR
         pass
 

lib/GenomeFileUtil/core/GenomeInterface.py

@@ -16,6 +16,10 @@
 
 MAX_GENOME_SIZE = 2**30
 
+# catalog params
+MAX_THREADS_DEFAULT = 10
+THREADS_PER_CPU_DEFAULT = 1
+
 
 class GenomeInterface:
     def __init__(self, config):

scripts/run_tests_within_container.sh

@@ -2,7 +2,8 @@
 script_dir=$(dirname "$(readlink -f "$0")")
 export KB_DEPLOYMENT_CONFIG=$script_dir/../deploy.cfg
 export KB_AUTH_TOKEN=`cat /kb/module/work/token`
-export PYTHONPATH=$script_dir/../lib:$PATH:$PYTHONPATH
+export PYTHONPATH=$script_dir/../lib:$PYTHONPATH
+export PYTHONPATH=$script_dir/../test:$PYTHONPATH
 
 # Set TEST_PATH to run a specific test. Eg: TEST_PATH=test.core.update_taxon_assignments_test
 export TEST_PATH=.

test/conftest.py

@@ -0,0 +1,7 @@
+import traceback
+
+
+def assert_exception_correct(got: Exception, expected: Exception):
+    err = "".join(traceback.TracebackException.from_exception(got).format())
+    assert got.args == expected.args, err
+    assert type(got) == type(expected)

test/genome_tests/impl_test.py

@@ -0,0 +1,52 @@
+import os
+import pytest
+import unittest
+
+from GenomeFileUtil.GenomeFileUtilImpl import GenomeFileUtil
+from conftest import assert_exception_correct
+
+
+class ImplTest(unittest.TestCase):
+    def setUp(self):
+        self.cfg = {}
+        self.cfg["workspace-url"] = "https://ci.kbase.us/services/ws"
+        self.cfg["shock-url"] = "https://ci.kbase.us/services/shock-api"
+        self.cfg["handle-service-url"] = "https://ci.kbase.us/services/handle_service"
+        self.cfg["scratch"] = "/kb/module/work/tmp"
+        self.cfg["srv-wiz-url"] = "https://ci.kbase.us/services/service_wizard"
+        self.cfg["auth-service-url"] = "https://ci.kbase.us/services/auth/api/legacy/KBase/Sessions/Login"
+        self.cfg["re-api-url"] = "https://ci.kbase.us/services/relation_engine_api"
+
+    def tearDown(self):
+        for kbase_secure_param in (
+            "KBASE_SECURE_CONFIG_PARAM_MAX_THREADS",
+            "KBASE_SECURE_CONFIG_PARAM_THREADS_PER_CPU",
+        ):
+            os.environ.pop(kbase_secure_param, None)
+
+    def _run_test_fail(self, cfg, error_message):
+        with pytest.raises(Exception) as got:
+            GenomeFileUtil(cfg)
+        assert_exception_correct(got.value, ValueError(error_message))
+
+    def test_valid_catalog_param_type(self):
+        os.environ["KBASE_SECURE_CONFIG_PARAM_MAX_THREADS"] = "16"
+        os.environ["KBASE_SECURE_CONFIG_PARAM_THREADS_PER_CPU"] = "2.5"
+        gfu = GenomeFileUtil(self.cfg)
+        self.assertEqual(gfu.max_threads, 16)
+        self.assertEqual(gfu.threads_per_cpu, 2.5)
+
+    def test_valid_default_catalog_param_type(self):
+        gfu = GenomeFileUtil(self.cfg)
+        self.assertEqual(gfu.max_threads, 10)
+        self.assertEqual(gfu.threads_per_cpu, 1)
+
+    def test_invalid_max_threads(self):
+        os.environ["KBASE_SECURE_CONFIG_PARAM_MAX_THREADS"] = "10.5"
+        os.environ["KBASE_SECURE_CONFIG_PARAM_THREADS_PER_CPU"] = "2.5"
+        self._run_test_fail(self.cfg, "MAX_THREADS must be of type int")
+
+    def test_invalid_threads_per_cpu(self):
+        os.environ["KBASE_SECURE_CONFIG_PARAM_MAX_THREADS"] = "10"
+        os.environ["KBASE_SECURE_CONFIG_PARAM_THREADS_PER_CPU"] = "2.8e"
+        self._run_test_fail(self.cfg, "THREADS_PER_CPU must be of type float")