--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/cwltool/tests/test_ext.py	Thu May 14 14:56:58 2020 -0400
@@ -0,0 +1,210 @@
+from __future__ import absolute_import
+
+import os
+import shutil
+import tempfile
+import sys
+import re
+from io import StringIO
+
+import pytest
+
+from cwltool.main import main
+import cwltool.process
+
+
+from .util import get_data, needs_docker, temp_dir, windows_needs_docker
+
+
+@needs_docker
+def test_missing_enable_ext():
+    # Require that --enable-ext is provided.
+    assert main([get_data('tests/wf/listing_deep.cwl'), get_data('tests/listing-job.yml')]) != 0
+
+@needs_docker
+def test_listing_deep():
+    params = ["--enable-ext", get_data('tests/wf/listing_deep.cwl'),
+              get_data('tests/listing-job.yml')]
+    assert main(params) == 0
+
+@needs_docker
+def test_cwltool_options():
+    try:
+        opt = os.environ.get("CWLTOOL_OPTIONS")
+        os.environ["CWLTOOL_OPTIONS"] = "--enable-ext"
+        params = [get_data('tests/wf/listing_deep.cwl'),
+                  get_data('tests/listing-job.yml')]
+        assert main(params) == 0
+    finally:
+        if opt is not None:
+            os.environ["CWLTOOL_OPTIONS"] = opt
+        else:
+            del os.environ["CWLTOOL_OPTIONS"]
+
+@needs_docker
+def test_listing_shallow():
+    # This fails on purpose, because it tries to access listing in a subdirectory
+    # the same way that listing_deep does, but it shouldn't be expanded.
+    params = ["--enable-ext", get_data('tests/wf/listing_shallow.cwl'),
+              get_data('tests/listing-job.yml')]
+    assert main(params) != 0
+
+@needs_docker
+def test_listing_none():
+    # This fails on purpose, because it tries to access listing but it shouldn't be there.
+    params = ["--enable-ext", get_data('tests/wf/listing_none.cwl'),
+              get_data('tests/listing-job.yml')]
+    assert main(params) != 0
+
+@needs_docker
+def test_listing_v1_0():
+    # Default behavior in 1.0 is deep expansion.
+    assert main([get_data('tests/wf/listing_v1_0.cwl'), get_data('tests/listing-job.yml')]) == 0
+
+@pytest.mark.skip(reason="This is not the default behaviour yet")
+@needs_docker
+def test_listing_v1_1():
+    # Default behavior in 1.1 will be no expansion
+    assert main([get_data('tests/wf/listing_v1_1.cwl'), get_data('tests/listing-job.yml')]) != 0
+
+@needs_docker
+def test_double_overwrite(tmpdir):
+    with temp_dir() as tmp:
+        tmp_name = os.path.join(tmp, "value")
+
+        before_value, expected_value = "1", "3"
+
+        with open(tmp_name, "w") as f:
+            f.write(before_value)
+
+        assert main(["--enable-ext", "--outdir", str(tmpdir),
+                     get_data('tests/wf/mut2.cwl'), "-a", tmp_name]) == 0
+
+        with open(tmp_name, "r") as f:
+            actual_value = f.read()
+
+        assert actual_value == expected_value
+
+@needs_docker
+def test_disable_file_overwrite_without_ext():
+    with temp_dir() as tmp:
+        with temp_dir() as out:
+            tmp_name = os.path.join(tmp, "value")
+            out_name = os.path.join(out, "value")
+
+            before_value, expected_value = "1", "2"
+
+            with open(tmp_name, "w") as f:
+                f.write(before_value)
+
+            assert main(["--outdir", out, get_data('tests/wf/updateval.cwl'), "-r", tmp_name]) == 0
+
+            with open(tmp_name, "r") as f:
+                tmp_value = f.read()
+            with open(out_name, "r") as f:
+                out_value = f.read()
+
+            assert tmp_value == before_value
+            assert out_value == expected_value
+
+@needs_docker
+def test_disable_dir_overwrite_without_ext():
+    with temp_dir() as tmp:
+        with temp_dir() as out:
+
+            assert main(["--outdir", out, get_data('tests/wf/updatedir.cwl'), "-r", tmp]) == 0
+
+            assert not os.listdir(tmp)
+            assert os.listdir(out)
+
+@needs_docker
+def test_disable_file_creation_in_outdir_with_ext():
+    with temp_dir() as tmp:
+        with temp_dir() as out:
+
+            tmp_name = os.path.join(tmp, "value")
+            out_name = os.path.join(out, "value")
+
+            before_value, expected_value = "1", "2"
+
+            with open(tmp_name, "w") as f:
+                f.write(before_value)
+
+            params = ["--enable-ext", "--leave-outputs", "--outdir",
+                      out, get_data('tests/wf/updateval_inplace.cwl'), "-r", tmp_name]
+            assert main(params) == 0
+
+            with open(tmp_name, "r") as f:
+                tmp_value = f.read()
+
+            assert tmp_value == expected_value
+            assert not os.path.exists(out_name)
+
+@needs_docker
+def test_disable_dir_creation_in_outdir_with_ext():
+    with temp_dir() as tmp:
+        with temp_dir() as out:
+            params = ["--enable-ext", "--leave-outputs", "--outdir",
+                      out, get_data('tests/wf/updatedir_inplace.cwl'), "-r", tmp]
+            assert main(params) == 0
+
+            assert os.listdir(tmp)
+            assert not os.listdir(out)
+
+@needs_docker
+def test_write_write_conflict():
+    with temp_dir('tmp') as tmp:
+        tmp_name = os.path.join(tmp, "value")
+
+        before_value, expected_value = "1", "2"
+
+        with open(tmp_name, "w") as f:
+            f.write(before_value)
+
+        assert main(["--enable-ext", get_data('tests/wf/mut.cwl'), "-a", tmp_name]) != 0
+
+        with open(tmp_name, "r") as f:
+            tmp_value = f.read()
+
+        assert tmp_value == expected_value
+
+@pytest.mark.skip(reason="This test is non-deterministic")
+def test_read_write_conflict():
+    with temp_dir('tmp') as tmp:
+        tmp_name = os.path.join(tmp, "value")
+
+        with open(tmp_name, "w") as f:
+            f.write("1")
+
+        assert main(["--enable-ext", get_data('tests/wf/mut3.cwl'), "-a", tmp_name]) != 0
+
+@needs_docker
+def test_require_prefix_networkaccess():
+    assert main(["--enable-ext", get_data('tests/wf/networkaccess.cwl')]) == 0
+    assert main([get_data('tests/wf/networkaccess.cwl')]) != 0
+    assert main(["--enable-ext", get_data('tests/wf/networkaccess-fail.cwl')]) != 0
+
+@needs_docker
+def test_require_prefix_workreuse(tmpdir):
+    assert main(["--enable-ext", '--outdir', str(tmpdir), get_data('tests/wf/workreuse.cwl')]) == 0
+    assert main([get_data('tests/wf/workreuse.cwl')]) != 0
+    assert main(["--enable-ext", get_data('tests/wf/workreuse-fail.cwl')]) != 0
+
+@windows_needs_docker
+def test_require_prefix_timelimit():
+    assert main(["--enable-ext", get_data('tests/wf/timelimit.cwl')]) == 0
+    assert main([get_data('tests/wf/timelimit.cwl')]) != 0
+    assert main(["--enable-ext", get_data('tests/wf/timelimit-fail.cwl')]) != 0
+
+def test_warn_large_inputs():
+    was = cwltool.process.FILE_COUNT_WARNING
+    try:
+        stream = StringIO()
+
+        cwltool.process.FILE_COUNT_WARNING = 3
+        main([get_data('tests/wf/listing_v1_0.cwl'), get_data('tests/listing2-job.yml')],
+             stderr=stream)
+
+        assert "Recursive directory listing has resulted in a large number of File" in re.sub("\n  *", " ", stream.getvalue())
+    finally:
+        cwltool.process.FILE_COUNT_WARNING = was