diff env/lib/python3.7/site-packages/cwltool/tests/test_toolargparse.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

--- a/env/lib/python3.7/site-packages/cwltool/tests/test_toolargparse.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,138 +0,0 @@
-import os
-import sys
-from tempfile import NamedTemporaryFile
-from io import BytesIO, StringIO
-
-import pytest
-from cwltool.main import main
-import cwltool.executors
-
-from .util import get_data, needs_docker
-
-script_a = '''
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
-class: CommandLineTool
-doc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"
-inputs:
-  #Give it a list of input files
-  - id: input
-    type: File
-    inputBinding:
-      position: 0
-outputs:
-  - id: output
-    type: File
-    outputBinding:
-      glob: test.txt
-stdout: test.txt
-baseCommand: [cat]
-'''
-
-script_b = '''
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
-class: CommandLineTool
-inputs:
-  - id: bdg
-    type: "boolean"
-outputs:
-  - id: output
-    type: File
-    outputBinding:
-      glob: foo
-baseCommand:
-  - echo
-  - "ff"
-stdout: foo
-'''
-
-script_c = '''
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
-class: ExpressionTool
-
-inputs:
-  foo:
-    type:
-      type: record
-      fields:
-        one: File
-        two: string
-
-expression: $(inputs.foo.two)
-
-outputs: []
-'''
-
-scripts_argparse_params = [
-    ('help', script_a,
-     lambda x: ["--debug", x, '--input', get_data('tests/echo.cwl')]
-     ),
-    ('boolean', script_b, lambda x: [x, '--help']
-     ),
-    ('help with c', script_c, lambda x: [x, '--help']),
-    ('foo with c', script_c,
-     lambda x: [x, '--foo.one', get_data('tests/echo.cwl'), '--foo.two', 'test']
-     )
-]
-
-@needs_docker
[e-mail]('name,script_contents,params', scripts_argparse_params)
-def test_argparse(name, script_contents, params, tmpdir):
-    script = None
-    try:
-        script = NamedTemporaryFile(mode='w', delete=False)
-        script.write(script_contents)
-        script.close()
-
-        my_params = ["--outdir", str(tmpdir)]
-        my_params.extend(params(script.name))
-        assert main(my_params) == 0, name
-
-    except SystemExit as err:
-        assert err.code == 0, name
-    finally:
-        if script and script.name and os.path.exists(script.name):
-            os.unlink(script.name)
-
-
-class NoopJobExecutor(cwltool.executors.JobExecutor):
-    def run_jobs(self,
-                 process,           # type: Process
-                 job_order_object,  # type: Dict[Text, Any]
-                 logger,            # type: logging.Logger
-                 runtime_context     # type: RuntimeContext
-                ):  # type: (...) -> None
-        pass
-
-    def execute(self,
-                process,           # type: Process
-                job_order_object,  # type: Dict[Text, Any]
-                runtime_context,   # type: RuntimeContext
-                logger=None,       # type: logging.Logger
-               ):  # type: (...) -> Tuple[Optional[Union[Dict[Text, Any], List[Dict[Text, Any]]]], Text]
-        return {}, "success"
-
-def test_dont_require_inputs():
-    if sys.version_info[0] < 3:
-        stream = BytesIO()
-    else:
-        stream = StringIO()
-
-    script = None
-    try:
-        script = NamedTemporaryFile(mode='w', delete=False)
-        script.write(script_a)
-        script.close()
-
-        assert main(argsl=["--debug", script.name, "--input", script.name], executor=NoopJobExecutor(), stdout=stream) == 0
-        assert main(argsl=["--debug", script.name], executor=NoopJobExecutor(), stdout=stream) == 2
-        assert main(argsl=["--debug", script.name], executor=NoopJobExecutor(), input_required=False, stdout=stream) == 0
-
-    except SystemExit as err:
-        assert err.code == 0, name
-    finally:
-        if script and script.name and os.path.exists(script.name):
-            os.unlink(script.name)