chore: rename to

pyproject.toml

@@ -17,8 +17,8 @@ classifiers = [
 ]
 
 [tool.poetry.scripts]
-filer = 'tesk.service.filer:main'
-taskmaster = 'tesk.service.taskmaster:main'
+filer = 'tesk.services.filer:main'
+taskmaster = 'tesk.services.taskmaster:main'
 
 [tool.poetry.dependencies]
 python = "^3.11"

tesk/service/filer.py → tesk/services/filer.py

@@ -15,15 +15,15 @@
 
 import requests
 
-from tesk.service.constants import TIMEOUT
-from tesk.service.exceptions import (
+from tesk.services.constants import TIMEOUT
+from tesk.services.exceptions import (
 	FileProtocolDisabled,
 	ServiceStatusCodes,
 	UnknownProtocol,
 )
-from tesk.service.filer_s3 import S3Transput
-from tesk.service.path import containerPath, fileEnabled, getPath
-from tesk.service.transput import Transput, Type, urlparse
+from tesk.services.filer_s3 import S3Transput
+from tesk.services.path import containerPath, fileEnabled, getPath
+from tesk.services.transput import Transput, Type, urlparse
 
 
 class HTTPTransput(Transput):

tesk/service/filer_class.py → tesk/services/filer_class.py

@@ -1,7 +1,7 @@
 import json
 
-from tesk.service import path
-from tesk.service.path import fileEnabled
+from tesk.services import path
+from tesk.services.path import fileEnabled
 
 
 class Filer:

tesk/service/filer_s3.py → tesk/services/filer_s3.py

@@ -6,7 +6,7 @@
 import boto3
 import botocore
 
-from tesk.service.transput import Transput, Type
+from tesk.services.transput import Transput, Type
 
 
 class S3Transput(Transput):

tesk/service/job.py → tesk/services/job.py

@@ -5,8 +5,8 @@
 from kubernetes import client
 from kubernetes.client.exceptions import ApiException
 
-from tesk.service.exceptions import ServiceStatusCodes
-from tesk.service.utils import pprint
+from tesk.services.exceptions import ServiceStatusCodes
+from tesk.services.utils import pprint
 
 logging.basicConfig(format='%(message)s', level=logging.INFO)
 

tesk/service/path.py → tesk/services/path.py

@@ -2,7 +2,7 @@
 from os.path import relpath
 from urllib.parse import urlparse
 
-from tesk.service.exceptions import InvalidHostPath
+from tesk.services.exceptions import InvalidHostPath
 
 
 def getEnv(varName):

tesk/service/pvc.py → tesk/services/pvc.py

@@ -4,8 +4,8 @@
 from kubernetes import client
 from kubernetes.client.exceptions import ApiException
 
-from tesk.service.exceptions import ServiceStatusCodes
-from tesk.service.utils import pprint
+from tesk.services.exceptions import ServiceStatusCodes
+from tesk.services.utils import pprint
 
 
 class PVC:

tesk/service/taskmaster.py → tesk/services/taskmaster.py

@@ -10,9 +10,9 @@
 
 from kubernetes import config
 
-from tesk.service.filer_class import Filer
-from tesk.service.job import Job
-from tesk.service.pvc import PVC
+from tesk.services.filer_class import Filer
+from tesk.services.job import Job
+from tesk.services.pvc import PVC
 
 created_jobs = []
 poll_interval = 5

tests/test_unit/test_service/FilerClassTest.py → tests/test_unit/test_services/FilerClassTest.py

@@ -1,19 +1,19 @@
 import os
 import unittest
 
-from tesk.service import path
-from tesk.service.filer_class import Filer
-from tesk.service.utils import pprint
+from tesk.services import path
+from tesk.services.filer_class import Filer
+from tesk.services.utils import pprint
 
 try:
 	from unittest.mock import patch  # Python 3 @UnresolvedImport
 except ImportError:
 	from unittest.mock import patch
 
 
-@patch('tesk.service.path.HOST_BASE_PATH', '/home/tfga/workspace/cwl-tes')
-@patch('tesk.service.path.CONTAINER_BASE_PATH', '/transfer')
-@patch('tesk.service.path.TRANSFER_PVC_NAME', 'transfer-pvc')
+@patch('tesk.services.path.HOST_BASE_PATH', '/home/tfga/workspace/cwl-tes')
+@patch('tesk.services.path.CONTAINER_BASE_PATH', '/transfer')
+@patch('tesk.services.path.TRANSFER_PVC_NAME', 'transfer-pvc')
 @patch.dict(
 	os.environ,
 	{

tests/test_unit/test_service/TaskMasterTest.py → tests/test_unit/test_services/TaskMasterTest.py

@@ -4,7 +4,7 @@
 from argparse import Namespace
 from unittest.mock import patch
 
-from tesk.service.taskmaster import newLogger, newParser, run_task
+from tesk.services.taskmaster import newLogger, newParser, run_task
 
 
 def pvcCreateMock(self):
@@ -74,13 +74,13 @@ def test_pullPolicyAlways(self):
 		)
 
 	@patch(
-		'tesk.service.taskmaster.args',
+		'tesk.services.taskmaster.args',
 		Namespace(debug=True, namespace='default', pull_policy_always=True),
 	)
-	@patch('tesk.service.taskmaster.logger', newLogger(logging.DEBUG))
-	@patch('tesk.service.taskmaster.PVC.create', pvcCreateMock)
-	@patch('tesk.service.taskmaster.PVC.delete', pvcDeleteMock)
-	@patch('tesk.service.taskmaster.Job.run_to_completion', jobRunToCompletionMock)
+	@patch('tesk.services.taskmaster.logger', newLogger(logging.DEBUG))
+	@patch('tesk.services.taskmaster.PVC.create', pvcCreateMock)
+	@patch('tesk.services.taskmaster.PVC.delete', pvcDeleteMock)
+	@patch('tesk.services.taskmaster.Job.run_to_completion', jobRunToCompletionMock)
 	def test_run_task(self):
 		with open('tests/resources/inputFile.json') as fh:
 			data = json.load(fh)

tests/test_unit/test_service/test_filer.py → tests/test_unit/test_services/test_filer.py

@@ -6,12 +6,12 @@
 
 from fs.opener import open_fs
 
-from tesk.service.exceptions import (
+from tesk.services.exceptions import (
 	FileProtocolDisabled,
 	InvalidHostPath,
 	UnknownProtocol,
 )
-from tesk.service.filer import (
+from tesk.services.filer import (
 	FileTransput,
 	FTPTransput,
 	HTTPTransput,
@@ -23,9 +23,9 @@
 	process_file,
 	subfolders_in,
 )
-from tesk.service.filer_s3 import S3Transput
-from tesk.service.path import containerPath
-from tests.test_unit.test_service.assertThrows import AssertThrowsMixin
+from tesk.services.filer_s3 import S3Transput
+from tesk.services.path import containerPath
+from tests.test_unit.test_services.assertThrows import AssertThrowsMixin
 
 
 def getTree(rootDir):
@@ -41,15 +41,15 @@ def stripLines(txt):
 	return '\n'.join([line.strip() for line in txt.splitlines()[1:]])
 
 
-@patch('tesk.service.path.HOST_BASE_PATH', '/home/tfga/workspace/cwl-tes')
-@patch('tesk.service.path.CONTAINER_BASE_PATH', '/transfer')
+@patch('tesk.services.path.HOST_BASE_PATH', '/home/tfga/workspace/cwl-tes')
+@patch('tesk.services.path.CONTAINER_BASE_PATH', '/transfer')
 class FilerTest(unittest.TestCase, AssertThrowsMixin):
 	@classmethod
 	def setUpClass(cls):
 		logConfig(logging.DEBUG)  # Doesn't work...
 
-	@patch('tesk.service.filer.copyDir')
-	@patch('tesk.service.filer.shutil.copy')
+	@patch('tesk.services.filer.copyDir')
+	@patch('tesk.services.filer.shutil.copy')
 	def test_download_file(self, copyMock, copyDirMock):
 		filedata = {
 			'url': 'file:///home/tfga/workspace/cwl-tes/tmphrtip1o8/md5',
@@ -69,8 +69,8 @@ def test_download_file(self, copyMock, copyDirMock):
 			'/var/lib/cwl/stgda974802-fa81-4f0b-' '8fe4-341d5655af4b/md5',
 		)
 
-	@patch('tesk.service.filer.copyDir')
-	@patch('tesk.service.filer.shutil.copy')
+	@patch('tesk.services.filer.copyDir')
+	@patch('tesk.services.filer.shutil.copy')
 	def test_download_dir(self, copyMock, copyDirMock):
 		filedata = {
 			'url': 'file:///home/tfga/workspace/cwl-tes/tmphrtip1o8/',
@@ -85,8 +85,8 @@ def test_download_dir(self, copyMock, copyDirMock):
 
 		copyDirMock.assert_called_once_with('/transfer/tmphrtip1o8', '/TclSZU')
 
-	@patch('tesk.service.filer.copyDir')
-	@patch('tesk.service.filer.shutil.copy')
+	@patch('tesk.services.filer.copyDir')
+	@patch('tesk.services.filer.shutil.copy')
 	def test_upload_dir(self, copyMock, copyDirMock):
 		filedata = {
 			'url': 'file:///home/tfga/workspace/cwl-tes/tmphrtip1o8/',
@@ -101,8 +101,8 @@ def test_upload_dir(self, copyMock, copyDirMock):
 
 		copyDirMock.assert_called_once_with('/TclSZU', '/transfer/tmphrtip1o8')
 
-	@patch('tesk.service.filer.copyDir')
-	@patch('tesk.service.filer.copyFile')
+	@patch('tesk.services.filer.copyDir')
+	@patch('tesk.services.filer.copyFile')
 	def test_upload_file(self, copyFileMock, copyDirMock):
 		filedata = {
 			'url': 'file:///home/tfga/workspace/cwl-tes/tmphrtip1o8/md5',
@@ -117,8 +117,8 @@ def test_upload_file(self, copyFileMock, copyDirMock):
 
 		copyFileMock.assert_called_once_with('/TclSZU/md5', '/transfer/tmphrtip1o8/md5')
 
-	@patch('tesk.service.filer.copyDir')
-	@patch('tesk.service.filer.copyFile')
+	@patch('tesk.services.filer.copyDir')
+	@patch('tesk.services.filer.copyFile')
 	def test_upload_file_glob(self, copyFileMock, copyDirMock):
 		filedata = {
 			'url': 'file:///home/tfga/workspace/cwl-tes/tmphrtip1o8/md5*',
@@ -139,7 +139,7 @@ def test_copyDir(self):
 		def rmDir(d):
 			os.system(f'rm -r {d}')
 
-		baseDir = 'tests/test_unit/test_service/resources/copyDirTest/'
+		baseDir = 'tests/test_unit/test_services/resources/copyDirTest/'
 		src = os.path.join(baseDir, 'src')
 		dst1 = os.path.join(baseDir, 'dst1')
 		dst2 = os.path.join(baseDir, 'dst2')

tests/test_unit/test_service/test_filer_ftp_pytest.py → tests/test_unit/test_services/test_filer_ftp_pytest.py

@@ -4,7 +4,7 @@
 import os
 from unittest import mock
 
-from tesk.service.filer import (
+from tesk.services.filer import (
 	FTPTransput,
 	Type,
 	ftp_check_directory,

tests/test_unit/test_service/test_filer_general_pytest.py → tests/test_unit/test_services/test_filer_general_pytest.py

@@ -7,7 +7,7 @@
 
 import pytest
 
-from tesk.service.filer import FileProtocolDisabled, copyContent, process_file
+from tesk.services.filer import FileProtocolDisabled, copyContent, process_file
 
 
 def test_process_file_no_scheme(caplog):
@@ -31,7 +31,7 @@ def test_process_file_with_scheme(mocker):
 		'path': '.',
 		'type': 'FILE',
 	}
-	mock_new_Trans = mocker.patch('tesk.service.filer.newTransput')
+	mock_new_Trans = mocker.patch('tesk.services.filer.newTransput')
 	process_file('inputs', filedata)
 
 	mock_new_Trans.assert_called_once_with('http', 'www.foo.bar')

tests/test_unit/test_service/test_filer_http_pytest.py → tests/test_unit/test_services/test_filer_http_pytest.py

@@ -4,10 +4,10 @@
 
 from requests import Response
 
-from tesk.service.filer import HTTPTransput, Type
+from tesk.services.filer import HTTPTransput, Type
 
 PATH_DOWN = 'test_download_file.txt'
-PATH_UP = 'tests/test_unit/test_service/test_filer_http_pytest.py'
+PATH_UP = 'tests/test_unit/test_services/test_filer_http_pytest.py'
 SUCCESS = 200
 FAIL = 300
 URL = 'http://www.foo.bar'

tests/test_unit/test_service/test_job.py → tests/test_unit/test_services/test_job.py

@@ -9,8 +9,8 @@
 from dateutil.tz import tzutc
 from kubernetes.client.rest import ApiException
 
-from tesk.service import taskmaster
-from tesk.service.job import Job
+from tesk.services import taskmaster
+from tesk.services.job import Job
 
 START_TIME = datetime.datetime.now(timezone.utc)
 
@@ -210,7 +210,7 @@ def test_job(self):
 
 	@patch('kubernetes.client.BatchV1Api.create_namespaced_job')
 	@patch(
-		'tesk.service.job.Job.get_status',
+		'tesk.services.job.Job.get_status',
 		side_effect=[
 			('Running', True),
 			('Running', True),
@@ -234,10 +234,10 @@ def test_run_to_completion_success(
 			)
 			self.assertEqual(status, 'Complete')
 
-	@patch('tesk.service.job.Job.delete')
-	@patch('tesk.service.taskmaster.check_cancelled', return_value=True)
+	@patch('tesk.services.job.Job.delete')
+	@patch('tesk.services.taskmaster.check_cancelled', return_value=True)
 	@patch('kubernetes.client.BatchV1Api.create_namespaced_job')
-	@patch('tesk.service.job.Job.get_status', side_effect=[('Running', True)])
+	@patch('tesk.services.job.Job.get_status', side_effect=[('Running', True)])
 	def test_run_to_completion_cancelled(
 		self,
 		mock_get_status,
@@ -258,12 +258,12 @@ def test_run_to_completion_cancelled(
 			)
 			self.assertEqual(status, 'Cancelled')
 
-	@patch('tesk.service.taskmaster.check_cancelled', return_value=False)
+	@patch('tesk.services.taskmaster.check_cancelled', return_value=False)
 	@patch(
 		'kubernetes.client.BatchV1Api.create_namespaced_job',
 		side_effect=ApiException(status=409, reason='conflict'),
 	)
-	@patch('tesk.service.job.Job.get_status', side_effect=[('Complete', True)])
+	@patch('tesk.services.job.Job.get_status', side_effect=[('Complete', True)])
 	@patch(
 		'kubernetes.client.BatchV1Api.read_namespaced_job',
 		side_effect=read_namespaced_job_running,
@@ -314,8 +314,8 @@ def test_run_to_completion_check_other_K8_exception(
 		'kubernetes.client.BatchV1Api.read_namespaced_job',
 		side_effect=read_namespaced_job_error,
 	)
-	@patch('tesk.service.job.Job.delete')
-	@patch('tesk.service.taskmaster.check_cancelled', return_value=False)
+	@patch('tesk.services.job.Job.delete')
+	@patch('tesk.services.taskmaster.check_cancelled', return_value=False)
 	@patch('kubernetes.client.BatchV1Api.create_namespaced_job')
 	def test_run_to_completion_error(  # noqa: PLR0913
 		self,

tests/test_unit/test_service/test_s3_filer.py → tests/test_unit/test_services/test_s3_filer.py

@@ -4,10 +4,10 @@
 import boto3
 import pytest
 
-# from tesk.service.extract_endpoint import extract_endpoint
+# from tesk.services.extract_endpoint import extract_endpoint
 from moto import mock_aws
 
-from tesk.service.filer_s3 import S3Transput
+from tesk.services.filer_s3 import S3Transput
 
 
 @pytest.fixture()
@@ -71,7 +71,7 @@ def test_check_if_bucket_exists(moto_boto, path, url, ftype, expected):
 	assert trans.check_if_bucket_exists(client) == expected
 
 
-# @patch('tesk.service.filer.os.makedirs')
+# @patch('tesk.services.filer.os.makedirs')
 # @patch('builtins.open')
 # @patch('s3transfer.utils.OSUtils.rename_file')
 @pytest.mark.parametrize(
@@ -93,10 +93,10 @@ def test_s3_download_file(moto_boto, path, url, ftype, expected, fs, caplog):  #
 			assert os.path.exists(path) is True
 
 
-@patch('tesk.service.filer.os.makedirs')
+@patch('tesk.services.filer.os.makedirs')
 @patch('builtins.open')
 @patch('s3transfer.utils.OSUtils.rename_file')
-# @patch("tesk.service.filer_s3.extract_endpoint", return_value="http://s3.amazonaws.com")
+# @patch("tesk.services.filer_s3.extract_endpoint", return_value="http://s3.amazonaws.com")
 @pytest.mark.parametrize(
 	'path, url, ftype,expected',
 	[
@@ -196,7 +196,7 @@ def test_upload_directory_for_unknown_file_type(moto_boto, fs, monkeypatch, capl
 	assert 'Object is neither file or directory' in caplog.text
 
 
-@patch('tesk.service.filer.os.path.exists', return_value=1)
+@patch('tesk.services.filer.os.path.exists', return_value=1)
 def test_extract_url_from_config_file(mock_path_exists):
 	"""
 	Testing extraction of endpoint url from default file location