toil 8.0.0__py3-none-any.whl → 8.2.0__py3-none-any.whl

toil-8.2.0.dist-info/RECORD

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+toil/wdl/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+toil/wdl/utils.py,sha256=U0TqbVTsap0VdeZjrUf4l71A7Zns-Hkso1B1Zdp2LRk,1316
+toil/wdl/wdltoil.py,sha256=wrkG23RYgDMi2LzoQwkGlUw5N22MiF1_uI8tAc92f20,248545
+toil-8.2.0.dist-info/licenses/LICENSE,sha256=YVxVi652J1ZDmtC3EMP5r0EbK85-hm_pzogiULmlqUA,12862
+toil-8.2.0.dist-info/METADATA,sha256=f6l9WgLeKx7-60wH5yHBgVo6ATCio82BrdXvwTZYoww,8687
+toil-8.2.0.dist-info/WHEEL,sha256=wXxTzcEDnjrTwFYjLPcsW_7_XihufBwmpiBeiXNBGEA,91
+toil-8.2.0.dist-info/entry_points.txt,sha256=EF2yFhV2UYuJGr-OjMkUOd3RyOCgRWQbS6XJtBJ25eM,436
+toil-8.2.0.dist-info/top_level.txt,sha256=1ydj7IXvHS9tMT5OVTSSpub6ZOaQeIn3KGCgJqaikF0,5
+toil-8.2.0.dist-info/RECORD,,

{toil-8.0.0.dist-info → toil-8.2.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (80.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

toil/test/lib/test_integration.py

@@ -1,104 +0,0 @@
-# Copyright (C) 2015-2024 Regents of the University of California
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import io
-import logging
-import pytest
-from typing import IO
-import urllib.request
-from urllib.error import URLError
-
-from toil.lib.retry import retry
-from toil.lib.integration import get_workflow_root_from_dockstore
-from toil.test import ToilTest, needs_online
-
-logger = logging.getLogger(__name__)
-logging.basicConfig(level=logging.DEBUG)
-
-@pytest.mark.integrative
-@needs_online
-class DockstoreLookupTest(ToilTest):
-    """
-    Make sure we can look up workflows on Dockstore.
-    """
-
-    @retry(errors=[URLError, RuntimeError])
-    def read_result(self, url_or_path: str) -> IO[bytes]:
-        """
-        Read a file or URL.
-
-        Binary mode to allow testing for binary file support.
-
-        This lets us test that we have the right workflow contents and not care
-        how we are being shown them.
-        """
-        if url_or_path.startswith("http://") or url_or_path.startswith("https://"):
-            response = urllib.request.urlopen(url_or_path)
-            if response.status != 200:
-                raise RuntimeError(f"HTTP error response: {response}")
-            return response
-        else:
-            return open(url_or_path, "rb")
-
-    # TODO: Tests that definitely test a clear cache
-
-    def test_lookup_from_page_url(self) -> None:
-        PAGE_URL = "https://dockstore.org/workflows/github.com/dockstore/bcc2020-training/HelloWorld:master?tab=info"
-        # If we go in through the website we get an extra refs/heads/ on the branch name.
-        WORKFLOW_URL = "https://raw.githubusercontent.com/dockstore/bcc2020-training/master/wdl-training/exercise1/HelloWorld.wdl"
-        looked_up = get_workflow_root_from_dockstore(PAGE_URL)
-
-        data_from_lookup = self.read_result(looked_up).read()
-        data_from_source = self.read_result(WORKFLOW_URL).read()
-        self.assertEqual(data_from_lookup, data_from_source)
-
-    def test_lookup_from_trs(self) -> None:
-        TRS_ID = "#workflow/github.com/dockstore-testing/md5sum-checker"
-        # Despite "-checker" in the ID, this actually refers to the base md5sum
-        # workflow that just happens to have a checker *available*, not to the
-        # checker workflow itself.
-        WORKFLOW_URL = "https://raw.githubusercontent.com/dockstore-testing/md5sum-checker/master/md5sum/md5sum-workflow.cwl"
-        looked_up = get_workflow_root_from_dockstore(TRS_ID)
-        
-        data_from_lookup = self.read_result(looked_up).read()
-        data_from_source = self.read_result(WORKFLOW_URL).read()
-        self.assertEqual(data_from_lookup, data_from_source)
-
-    def test_lookup_from_trs_cached(self) -> None:
-        TRS_ID = "#workflow/github.com/dockstore-testing/md5sum-checker"
-        WORKFLOW_URL = "https://raw.githubusercontent.com/dockstore-testing/md5sum-checker/master/md5sum/md5sum-workflow.cwl"
-        # This lookup may or may not be cached
-        get_workflow_root_from_dockstore(TRS_ID)
-        # This lookup is definitely cached
-        looked_up = get_workflow_root_from_dockstore(TRS_ID)
-        
-        data_from_lookup = self.read_result(looked_up).read()
-        data_from_source = self.read_result(WORKFLOW_URL).read()
-        self.assertEqual(data_from_lookup, data_from_source)
-
-    def test_lookup_from_trs_with_version(self) -> None:
-        TRS_ID = "#workflow/github.com/dockstore-testing/md5sum-checker:workflowWithHTTPImport"
-        WORKFLOW_URL = "https://raw.githubusercontent.com/dockstore-testing/md5sum-checker/workflowWithHTTPImport/md5sum/md5sum-workflow.cwl"
-        looked_up = get_workflow_root_from_dockstore(TRS_ID)
-        
-        data_from_lookup = self.read_result(looked_up).read()
-        data_from_source = self.read_result(WORKFLOW_URL).read()
-        self.assertEqual(data_from_lookup, data_from_source)
-
-    def test_lookup_from_trs_nonexistent_version(self) -> None:
-        TRS_ID = "#workflow/github.com/dockstore-testing/md5sum-checker:notARealVersion"
-        with self.assertRaises(RuntimeError):
-            looked_up = get_workflow_root_from_dockstore(TRS_ID)
-
-