Makefile

@@ -175,4 +175,18 @@ mypy3: ${PYSOURCES}
 		 --warn-redundant-casts \
 		 cwltool
 
+release: FORCE
+	./release-test.sh
+	. testenv2/bin/activate && \
+		testenv2/src/${MODULE}/setup.py sdist bdist_wheel && \
+		pip install twine && \
+		twine upload testenv2/src/${MODULE}/dist/* && \
+		git tag ${VERSION} && git push --tags
+
 FORCE:
+
+# Use this to print the value of a Makefile variable
+# Example `make print-VERSION`
+# From https://www.cmcrossroads.com/article/printing-value-makefile-variable
+print-%  : ; @echo $* = $($*)
+

PKG-INFO

 Metadata-Version: 1.1
 Name: cwltool
-Version: 1.0.20171221100033
+Version: 1.0.20180211183944
 Summary: Common workflow language reference implementation
 Home-page: https://github.com/common-workflow-language/cwltool
 Author: Common workflow language working group
@@ -123,20 +123,31 @@ Description: ==================================================================
         .. |Build Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance
            :target: https://ci.commonwl.org/job/cwltool-conformance/
         
-        Running user-space implementations of Docker
-        --------------------------------------------
+        Using user-space replacements for Docker
+        ----------------------------------------
         
-        Some compute environments disallow user-space installation of Docker due to incompatiblities in libraries or to meet security requirements. The CWL reference supports using a user space implementation with the `--user-space-docker-cmd` option.
+        Some shared computing environments don't support Docker software containers for technical or policy reasons.
+        As a work around, the CWL reference runner supports using a alternative ``docker`` implementations on Linux
+        with the ``--user-space-docker-cmd`` option.
         
-        Example using `dx-docker` (https://wiki.dnanexus.com/Developer-Tutorials/Using-Docker-Images):
+        One such "user space" friendly docker replacement is ``udocker`` https://github.com/indigo-dc/udocker and another
+        is ``dx-docker`` https://wiki.dnanexus.com/Developer-Tutorials/Using-Docker-Images
         
-        For use on Linux, install the DNAnexus toolkit (see https://wiki.dnanexus.com/Downloads for instructions).
+        udocker installation: https://github.com/indigo-dc/udocker/blob/master/doc/installation_manual.md#22-install-from-indigo-datacloud-repositories
+        
+        dx-docker installation: start with the DNAnexus toolkit (see https://wiki.dnanexus.com/Downloads for instructions).
         
         Run `cwltool` just as you normally would, but with the new option, e.g. from the conformance tests:
         
         .. code:: bash
         
-          cwltool --user-space-docker-cmd=dx-docker --outdir=/tmp/tmpidytmp v1.0/test-cwl-out2.cwl v1.0/empty.json
+          cwltool --user-space-docker-cmd=udocker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
+          
+        or 
+        
+        .. code:: bash
+        
+          cwltool --user-space-docker-cmd=dx-docker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
         
         Tool or workflow loading from remote or local locations
         -------------------------------------------------------
@@ -234,7 +245,7 @@ Description: ==================================================================
         
         .. code:: yaml
         
-          - type: module
+          - type: modules
         
         The outer list indicates that one plugin is being enabled, the plugin parameters are
         defined as a dictionary for this one list item. There is only one required parameter
@@ -409,18 +420,17 @@ Description: ==================================================================
         underlying workflow, cwltool supports requirement "overrides".
         
         The format of the "overrides" object is a mapping of item identifier (workflow,
-        workflow step, or command line tool) followed by a list of ProcessRequirements
-        that should be applied.
+        workflow step, or command line tool) to the process requirements that should be applied.
         
         .. code:: yaml
         
           cwltool:overrides:
             echo.cwl:
-              - class: EnvVarRequirement
+              requirements:
+                EnvVarRequirement:
                   envDef:
                     MESSAGE: override_value
         
-        
         Overrides can be specified either on the command line, or as part of the job
         input document.  Workflow steps are identified using the name of the workflow
         file followed by the step name as a document fragment identifier "#id".
@@ -436,7 +446,8 @@ Description: ==================================================================
           input_parameter2: value2
           cwltool:overrides:
             workflow.cwl#step1:
-              - class: EnvVarRequirement
+              requirements:
+                EnvVarRequirement:
                   envDef:
                     MESSAGE: override_value
         

README.rst

@@ -113,20 +113,31 @@ and ``--tmp-outdir-prefix`` to somewhere under ``/Users``::
 .. |Build Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-Running user-space implementations of Docker
---------------------------------------------
+Using user-space replacements for Docker
+----------------------------------------
 
-Some compute environments disallow user-space installation of Docker due to incompatiblities in libraries or to meet security requirements. The CWL reference supports using a user space implementation with the `--user-space-docker-cmd` option.
+Some shared computing environments don't support Docker software containers for technical or policy reasons.
+As a work around, the CWL reference runner supports using a alternative ``docker`` implementations on Linux
+with the ``--user-space-docker-cmd`` option.
 
-Example using `dx-docker` (https://wiki.dnanexus.com/Developer-Tutorials/Using-Docker-Images):
+One such "user space" friendly docker replacement is ``udocker`` https://github.com/indigo-dc/udocker and another
+is ``dx-docker`` https://wiki.dnanexus.com/Developer-Tutorials/Using-Docker-Images
 
-For use on Linux, install the DNAnexus toolkit (see https://wiki.dnanexus.com/Downloads for instructions).
+udocker installation: https://github.com/indigo-dc/udocker/blob/master/doc/installation_manual.md#22-install-from-indigo-datacloud-repositories
+
+dx-docker installation: start with the DNAnexus toolkit (see https://wiki.dnanexus.com/Downloads for instructions).
 
 Run `cwltool` just as you normally would, but with the new option, e.g. from the conformance tests:
 
 .. code:: bash
 
-  cwltool --user-space-docker-cmd=dx-docker --outdir=/tmp/tmpidytmp v1.0/test-cwl-out2.cwl v1.0/empty.json
+  cwltool --user-space-docker-cmd=udocker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
+  
+or 
+
+.. code:: bash
+
+  cwltool --user-space-docker-cmd=dx-docker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
 
 Tool or workflow loading from remote or local locations
 -------------------------------------------------------
@@ -224,7 +235,7 @@ the correct module environment before executing the above tool would simply be:
 
 .. code:: yaml
 
-  - type: module
+  - type: modules
 
 The outer list indicates that one plugin is being enabled, the plugin parameters are
 defined as a dictionary for this one list item. There is only one required parameter
@@ -399,18 +410,17 @@ environment or with a particular dataset.  To avoid the need to modify the
 underlying workflow, cwltool supports requirement "overrides".
 
 The format of the "overrides" object is a mapping of item identifier (workflow,
-workflow step, or command line tool) followed by a list of ProcessRequirements
-that should be applied.
+workflow step, or command line tool) to the process requirements that should be applied.
 
 .. code:: yaml
 
   cwltool:overrides:
     echo.cwl:
-      - class: EnvVarRequirement
+      requirements:
+        EnvVarRequirement:
           envDef:
             MESSAGE: override_value
 
-
 Overrides can be specified either on the command line, or as part of the job
 input document.  Workflow steps are identified using the name of the workflow
 file followed by the step name as a document fragment identifier "#id".
@@ -426,7 +436,8 @@ Override identifiers are relative to the toplevel workflow document.
   input_parameter2: value2
   cwltool:overrides:
     workflow.cwl#step1:
-      - class: EnvVarRequirement
+      requirements:
+        EnvVarRequirement:
           envDef:
             MESSAGE: override_value
 

cwltool.egg-info/PKG-INFO

 Metadata-Version: 1.1
 Name: cwltool
-Version: 1.0.20171221100033
+Version: 1.0.20180211183944
 Summary: Common workflow language reference implementation
 Home-page: https://github.com/common-workflow-language/cwltool
 Author: Common workflow language working group
@@ -123,20 +123,31 @@ Description: ==================================================================
         .. |Build Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance
            :target: https://ci.commonwl.org/job/cwltool-conformance/
         
-        Running user-space implementations of Docker
-        --------------------------------------------
+        Using user-space replacements for Docker
+        ----------------------------------------
         
-        Some compute environments disallow user-space installation of Docker due to incompatiblities in libraries or to meet security requirements. The CWL reference supports using a user space implementation with the `--user-space-docker-cmd` option.
+        Some shared computing environments don't support Docker software containers for technical or policy reasons.
+        As a work around, the CWL reference runner supports using a alternative ``docker`` implementations on Linux
+        with the ``--user-space-docker-cmd`` option.
         
-        Example using `dx-docker` (https://wiki.dnanexus.com/Developer-Tutorials/Using-Docker-Images):
+        One such "user space" friendly docker replacement is ``udocker`` https://github.com/indigo-dc/udocker and another
+        is ``dx-docker`` https://wiki.dnanexus.com/Developer-Tutorials/Using-Docker-Images
         
-        For use on Linux, install the DNAnexus toolkit (see https://wiki.dnanexus.com/Downloads for instructions).
+        udocker installation: https://github.com/indigo-dc/udocker/blob/master/doc/installation_manual.md#22-install-from-indigo-datacloud-repositories
+        
+        dx-docker installation: start with the DNAnexus toolkit (see https://wiki.dnanexus.com/Downloads for instructions).
         
         Run `cwltool` just as you normally would, but with the new option, e.g. from the conformance tests:
         
         .. code:: bash
         
-          cwltool --user-space-docker-cmd=dx-docker --outdir=/tmp/tmpidytmp v1.0/test-cwl-out2.cwl v1.0/empty.json
+          cwltool --user-space-docker-cmd=udocker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
+          
+        or 
+        
+        .. code:: bash
+        
+          cwltool --user-space-docker-cmd=dx-docker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
         
         Tool or workflow loading from remote or local locations
         -------------------------------------------------------
@@ -234,7 +245,7 @@ Description: ==================================================================
         
         .. code:: yaml
         
-          - type: module
+          - type: modules
         
         The outer list indicates that one plugin is being enabled, the plugin parameters are
         defined as a dictionary for this one list item. There is only one required parameter
@@ -409,18 +420,17 @@ Description: ==================================================================
         underlying workflow, cwltool supports requirement "overrides".
         
         The format of the "overrides" object is a mapping of item identifier (workflow,
-        workflow step, or command line tool) followed by a list of ProcessRequirements
-        that should be applied.
+        workflow step, or command line tool) to the process requirements that should be applied.
         
         .. code:: yaml
         
           cwltool:overrides:
             echo.cwl:
-              - class: EnvVarRequirement
+              requirements:
+                EnvVarRequirement:
                   envDef:
                     MESSAGE: override_value
         
-        
         Overrides can be specified either on the command line, or as part of the job
         input document.  Workflow steps are identified using the name of the workflow
         file followed by the step name as a document fragment identifier "#id".
@@ -436,7 +446,8 @@ Description: ==================================================================
           input_parameter2: value2
           cwltool:overrides:
             workflow.cwl#step1:
-              - class: EnvVarRequirement
+              requirements:
+                EnvVarRequirement:
                   envDef:
                     MESSAGE: override_value
         

cwltool.egg-info/SOURCES.txt

@@ -7,6 +7,7 @@ setup.cfg
 setup.py
 cwltool/__init__.py
 cwltool/__main__.py
+cwltool/argparser.py
 cwltool/builder.py
 cwltool/cwlNodeEngine.js
 cwltool/cwlNodeEngineJSConsole.js

cwltool/argparser.py

+from __future__ import absolute_import
+from __future__ import print_function
+
+import argparse
+import logging
+import os
+
+from typing import (Any, AnyStr, Dict, List, Sequence, Text, Union, cast)
+
+from schema_salad.ref_resolver import file_uri
+from .process import (Process, shortname)
+from .resolver import ga4gh_tool_registries
+from .software_requirements import (SOFTWARE_REQUIREMENTS_ENABLED)
+
+_logger = logging.getLogger("cwltool")
+
+defaultStreamHandler = logging.StreamHandler()
+_logger.addHandler(defaultStreamHandler)
+_logger.setLevel(logging.INFO)
+
+
+def arg_parser():  # type: () -> argparse.ArgumentParser
+    parser = argparse.ArgumentParser(description='Reference executor for Common Workflow Language')
+    parser.add_argument("--basedir", type=Text)
+    parser.add_argument("--outdir", type=Text, default=os.path.abspath('.'),
+                        help="Output directory, default current directory")
+
+    parser.add_argument("--no-container", action="store_false", default=True,
+                        help="Do not execute jobs in a Docker container, even when specified by the CommandLineTool",
+                        dest="use_container")
+
+    parser.add_argument("--preserve-environment", type=Text, action="append",
+                        help="Preserve specific environment variable when running CommandLineTools.  May be provided multiple times.",
+                        metavar="ENVVAR",
+                        default=["PATH"],
+                        dest="preserve_environment")
+
+    parser.add_argument("--preserve-entire-environment", action="store_true",
+                        help="Preserve entire parent environment when running CommandLineTools.",
+                        default=False,
+                        dest="preserve_entire_environment")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--rm-container", action="store_true", default=True,
+                         help="Delete Docker container used by jobs after they exit (default)",
+                         dest="rm_container")
+
+    exgroup.add_argument("--leave-container", action="store_false",
+                         default=True, help="Do not delete Docker container used by jobs after they exit",
+                         dest="rm_container")
+
+    cidgroup = parser.add_argument_group("Options for recording the Docker "
+        "container identifier into a file")
+    cidgroup.add_argument("--record-container-id", action="store_true",
+                          default=False,
+                          help="If enabled, store the Docker container ID into a file. "
+                          "See --cidfile-dir to specify the directory.",
+                          dest="record_container_id")
+
+    cidgroup.add_argument("--cidfile-dir", type=Text,
+                        help="Directory for storing the Docker container ID file. "
+                             "The default is the current directory",
+                        default="",
+                        dest="cidfile_dir")
+
+    cidgroup.add_argument("--cidfile-prefix", type=Text,
+                        help="Specify a prefix to the container ID filename. "
+                             "Final file name will be followed by a timestamp. "
+                             "The default is no prefix.",
+                        default="",
+                        dest="cidfile_prefix")
+
+    parser.add_argument("--tmpdir-prefix", type=Text,
+                        help="Path prefix for temporary directories",
+                        default="tmp")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--tmp-outdir-prefix", type=Text,
+                         help="Path prefix for intermediate output directories",
+                         default="tmp")
+
+    exgroup.add_argument("--cachedir", type=Text, default="",
+                         help="Directory to cache intermediate workflow outputs to avoid recomputing steps.")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--rm-tmpdir", action="store_true", default=True,
+                         help="Delete intermediate temporary directories (default)",
+                         dest="rm_tmpdir")
+
+    exgroup.add_argument("--leave-tmpdir", action="store_false",
+                         default=True, help="Do not delete intermediate temporary directories",
+                         dest="rm_tmpdir")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--move-outputs", action="store_const", const="move", default="move",
+                         help="Move output files to the workflow output directory and delete intermediate output directories (default).",
+                         dest="move_outputs")
+
+    exgroup.add_argument("--leave-outputs", action="store_const", const="leave", default="move",
+                         help="Leave output files in intermediate output directories.",
+                         dest="move_outputs")
+
+    exgroup.add_argument("--copy-outputs", action="store_const", const="copy", default="move",
+                         help="Copy output files to the workflow output directory, don't delete intermediate output directories.",
+                         dest="move_outputs")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--enable-pull", default=True, action="store_true",
+                         help="Try to pull Docker images", dest="enable_pull")
+
+    exgroup.add_argument("--disable-pull", default=True, action="store_false",
+                         help="Do not try to pull Docker images", dest="enable_pull")
+
+    parser.add_argument("--rdf-serializer",
+                        help="Output RDF serialization format used by --print-rdf (one of turtle (default), n3, nt, xml)",
+                        default="turtle")
+
+    parser.add_argument("--eval-timeout",
+                        help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
+                        type=float,
+                        default=20)
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--print-rdf", action="store_true",
+                         help="Print corresponding RDF graph for workflow and exit")
+    exgroup.add_argument("--print-dot", action="store_true",
+                         help="Print workflow visualization in graphviz format and exit")
+    exgroup.add_argument("--print-pre", action="store_true", help="Print CWL document after preprocessing.")
+    exgroup.add_argument("--print-deps", action="store_true", help="Print CWL document dependencies.")
+    exgroup.add_argument("--print-input-deps", action="store_true", help="Print input object document dependencies.")
+    exgroup.add_argument("--pack", action="store_true", help="Combine components into single document and print.")
+    exgroup.add_argument("--version", action="store_true", help="Print version and exit")
+    exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
+    exgroup.add_argument("--print-supported-versions", action="store_true", help="Print supported CWL specs.")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--strict", action="store_true",
+                         help="Strict validation (unrecognized or out of place fields are error)",
+                         default=True, dest="strict")
+    exgroup.add_argument("--non-strict", action="store_false", help="Lenient validation (ignore unrecognized fields)",
+                         default=True, dest="strict")
+
+    parser.add_argument("--skip-schemas", action="store_true",
+            help="Skip loading of schemas", default=True, dest="skip_schemas")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--verbose", action="store_true", help="Default logging")
+    exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
+    exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
+
+    parser.add_argument("--timestamps", action="store_true", help="Add "
+                        "timestamps to the errors, warnings, and "
+                        "notifications.")
+    parser.add_argument("--js-console", action="store_true", help="Enable javascript console output")
+    parser.add_argument("--user-space-docker-cmd",
+                        help="(Linux/OS X only) Specify a user space docker "
+                        "command (like udocker or dx-docker) that will be "
+                        "used to call 'pull' and 'run'")
+
+    dependency_resolvers_configuration_help = argparse.SUPPRESS
+    dependencies_directory_help = argparse.SUPPRESS
+    use_biocontainers_help = argparse.SUPPRESS
+    conda_dependencies = argparse.SUPPRESS
+
+    if SOFTWARE_REQUIREMENTS_ENABLED:
+        dependency_resolvers_configuration_help = "Dependency resolver configuration file describing how to adapt 'SoftwareRequirement' packages to current system."
+        dependencies_directory_help = "Defaut root directory used by dependency resolvers configuration."
+        use_biocontainers_help = "Use biocontainers for tools without an explicitly annotated Docker container."
+        conda_dependencies = "Short cut to use Conda to resolve 'SoftwareRequirement' packages."
+
+    parser.add_argument("--beta-dependency-resolvers-configuration", default=None, help=dependency_resolvers_configuration_help)
+    parser.add_argument("--beta-dependencies-directory", default=None, help=dependencies_directory_help)
+    parser.add_argument("--beta-use-biocontainers", default=None, help=use_biocontainers_help, action="store_true")
+    parser.add_argument("--beta-conda-dependencies", default=None, help=conda_dependencies, action="store_true")
+
+    parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
+
+    parser.add_argument("--relative-deps", choices=['primary', 'cwd'],
+                        default="primary", help="When using --print-deps, print paths "
+                                                "relative to primary file or current working directory.")
+
+    parser.add_argument("--enable-dev", action="store_true",
+                        help="Enable loading and running development versions "
+                             "of CWL spec.", default=False)
+
+    parser.add_argument("--enable-ext", action="store_true",
+                        help="Enable loading and running cwltool extensions "
+                             "to CWL spec.", default=False)
+
+    parser.add_argument("--default-container",
+                        help="Specify a default docker container that will be used if the workflow fails to specify one.")
+    parser.add_argument("--no-match-user", action="store_true",
+                        help="Disable passing the current uid to 'docker run --user`")
+    parser.add_argument("--disable-net", action="store_true",
+                        help="Use docker's default networking for containers;"
+                             " the default is to enable networking.")
+    parser.add_argument("--custom-net", type=Text,
+                        help="Will be passed to `docker run` as the '--net' "
+                             "parameter. Implies '--enable-net'.")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--enable-ga4gh-tool-registry", action="store_true", help="Enable resolution using GA4GH tool registry API",
+                        dest="enable_ga4gh_tool_registry", default=True)
+    exgroup.add_argument("--disable-ga4gh-tool-registry", action="store_false", help="Disable resolution using GA4GH tool registry API",
+                        dest="enable_ga4gh_tool_registry", default=True)
+
+    parser.add_argument("--add-ga4gh-tool-registry", action="append", help="Add a GA4GH tool registry endpoint to use for resolution, default %s" % ga4gh_tool_registries,
+                        dest="ga4gh_tool_registries", default=[])
+
+    parser.add_argument("--on-error",
+                        help="Desired workflow behavior when a step fails.  One of 'stop' or 'continue'. "
+                             "Default is 'stop'.", default="stop", choices=("stop", "continue"))
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--compute-checksum", action="store_true", default=True,
+                         help="Compute checksum of contents while collecting outputs",
+                         dest="compute_checksum")
+    exgroup.add_argument("--no-compute-checksum", action="store_false",
+                         help="Do not compute checksum of contents while collecting outputs",
+                         dest="compute_checksum")
+
+    parser.add_argument("--relax-path-checks", action="store_true",
+                        default=False, help="Relax requirements on path names to permit "
+                        "spaces and hash characters.", dest="relax_path_checks")
+    exgroup.add_argument("--make-template", action="store_true",
+                         help="Generate a template input object")
+
+    parser.add_argument("--force-docker-pull", action="store_true",
+                        default=False, help="Pull latest docker image even if"
+                                            " it is locally present", dest="force_docker_pull")
+    parser.add_argument("--no-read-only", action="store_true",
+                        default=False, help="Do not set root directory in the"
+                                            " container as read-only", dest="no_read_only")
+
+    parser.add_argument("--overrides", type=str,
+                        default=None, help="Read process requirement overrides from file.")
+
+    parser.add_argument("workflow", type=Text, nargs="?", default=None)
+    parser.add_argument("job_order", nargs=argparse.REMAINDER)
+
+    return parser
+
+
+def get_default_args():
+    # type: () -> Dict[str, Any]
+    """
+    Get default values of cwltool's command line options
+    """
+    ap = arg_parser()
+    args = ap.parse_args()
+    return vars(args)
+
+
+class FSAction(argparse.Action):
+    objclass = None  # type: Text
+
+    def __init__(self, option_strings, dest, nargs=None, **kwargs):
+        # type: (List[Text], Text, Any, **Any) -> None
+        if nargs is not None:
+            raise ValueError("nargs not allowed")
+        super(FSAction, self).__init__(option_strings, dest, **kwargs)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        # type: (argparse.ArgumentParser, argparse.Namespace, Union[AnyStr, Sequence[Any], None], AnyStr) -> None
+        setattr(namespace,
+                self.dest,  # type: ignore
+                {"class": self.objclass,
+                 "location": file_uri(str(os.path.abspath(cast(AnyStr, values))))})
+
+
+class FSAppendAction(argparse.Action):
+    objclass = None  # type: Text
+
+    def __init__(self, option_strings, dest, nargs=None, **kwargs):
+        # type: (List[Text], Text, Any, **Any) -> None
+        if nargs is not None:
+            raise ValueError("nargs not allowed")
+        super(FSAppendAction, self).__init__(option_strings, dest, **kwargs)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        # type: (argparse.ArgumentParser, argparse.Namespace, Union[AnyStr, Sequence[Any], None], AnyStr) -> None
+        g = getattr(namespace,
+                    self.dest  # type: ignore
+                    )
+        if not g:
+            g = []
+            setattr(namespace,
+                    self.dest,  # type: ignore
+                    g)
+        g.append(
+            {"class": self.objclass,
+             "location": file_uri(str(os.path.abspath(cast(AnyStr, values))))})
+
+
+class FileAction(FSAction):
+    objclass = "File"
+
+
+class DirectoryAction(FSAction):
+    objclass = "Directory"
+
+
+class FileAppendAction(FSAppendAction):
+    objclass = "File"
+
+
+class DirectoryAppendAction(FSAppendAction):
+    objclass = "Directory"
+
+
+def add_argument(toolparser, name, inptype, records, description="",
+                 default=None):
+    # type: (argparse.ArgumentParser, Text, Any, List[Text], Text, Any) -> None
+    if len(name) == 1:
+        flag = "-"
+    else:
+        flag = "--"
+
+    required = True
+    if isinstance(inptype, list):
+        if inptype[0] == "null":
+            required = False
+            if len(inptype) == 2:
+                inptype = inptype[1]
+            else:
+                _logger.debug(u"Can't make command line argument from %s", inptype)
+                return None
+
+    ahelp = description.replace("%", "%%")
+    action = None  # type: Union[argparse.Action, Text]
+    atype = None  # type: Any
+
+    if inptype == "File":
+        action = cast(argparse.Action, FileAction)
+    elif inptype == "Directory":
+        action = cast(argparse.Action, DirectoryAction)
+    elif isinstance(inptype, dict) and inptype["type"] == "array":
+        if inptype["items"] == "File":
+            action = cast(argparse.Action, FileAppendAction)
+        elif inptype["items"] == "Directory":
+            action = cast(argparse.Action, DirectoryAppendAction)
+        else:
+            action = "append"
+    elif isinstance(inptype, dict) and inptype["type"] == "enum":
+        atype = Text
+    elif isinstance(inptype, dict) and inptype["type"] == "record":
+        records.append(name)
+        for field in inptype['fields']:
+            fieldname = name + "." + shortname(field['name'])
+            fieldtype = field['type']
+            fielddescription = field.get("doc", "")
+            add_argument(
+                toolparser, fieldname, fieldtype, records,
+                fielddescription)
+        return
+    if inptype == "string":
+        atype = Text
+    elif inptype == "int":
+        atype = int
+    elif inptype == "double":
+        atype = float
+    elif inptype == "float":
+        atype = float
+    elif inptype == "boolean":
+        action = "store_true"
+
+    if default:
+        required = False
+
+    if not atype and not action:
+        _logger.debug(u"Can't make command line argument from %s", inptype)
+        return None
+
+    if inptype != "boolean":
+        typekw = {'type': atype}
+    else:
+        typekw = {}
+
+    toolparser.add_argument(  # type: ignore
+        flag + name, required=required, help=ahelp, action=action,
+        default=default, **typekw)
+
+
+def generate_parser(toolparser, tool, namemap, records):
+    # type: (argparse.ArgumentParser, Process, Dict[Text, Text], List[Text]) -> argparse.ArgumentParser
+    toolparser.add_argument("job_order", nargs="?", help="Job input json file")
+    namemap["job_order"] = "job_order"
+
+    for inp in tool.tool["inputs"]:
+        name = shortname(inp["id"])
+        namemap[name.replace("-", "_")] = name
+        inptype = inp["type"]
+        description = inp.get("doc", "")
+        default = inp.get("default", None)
+        add_argument(toolparser, name, inptype, records, description, default)
+
+    return toolparser

cwltool/builder.py

@@ -230,7 +230,7 @@ class Builder(object):
             return [prefix] if prefix else []
         elif value is True and prefix:
             return [prefix]
-        elif value is False or value is None:
+        elif value is False or value is None or (value is True and not prefix):
             return []
         else:
             l = [value]
@@ -251,7 +251,8 @@ class Builder(object):
                 return {k: self.do_eval(v, context, pull_image, recursive) for k, v in iteritems(ex)}
             if isinstance(ex, list):
                 return [self.do_eval(v, context, pull_image, recursive) for v in ex]
-
+        if context is None and type(ex) is str and "self" in ex:
+            return None
         return expression.do_eval(ex, self.job, self.requirements,
                                   self.outdir, self.tmpdir,
                                   self.resources,

cwltool/factory.py

@@ -4,6 +4,7 @@ from typing import Callable as tCallable
 from typing import Any, Dict, Text, Tuple, Union
 
 from . import load_tool, main, workflow
+from .argparser import get_default_args
 from .process import Process
 
 
@@ -41,7 +42,13 @@ class Factory(object):
         # type: (...) -> None
         self.makeTool = makeTool
         self.executor = executor
-        self.execkwargs = execkwargs
+
+        kwargs = get_default_args()
+        kwargs.pop("job_order")
+        kwargs.pop("workflow")
+        kwargs.pop("outdir")
+        kwargs.update(execkwargs)
+        self.execkwargs = kwargs
 
     def make(self, cwl):
         """Instantiate a CWL object from a CWl document."""

cwltool/job.py

 from __future__ import absolute_import
+import codecs
 import functools
 import io
 import json
@@ -10,6 +11,7 @@ import stat
 import subprocess
 import sys
 import tempfile
+import datetime
 from io import open
 from typing import (IO, Any, Callable, Dict, Iterable, List, MutableMapping, Text,
                     Tuple, Union, cast)
@@ -340,7 +342,7 @@ class DockerCommandLineJob(JobBase):
                     ensure_writable(host_outdir_tgt)
             elif vol.type == "WritableDirectory":
                 if vol.resolved.startswith("_:"):
-                    os.makedirs(vol.target, 0o0755)
+                    os.makedirs(host_outdir_tgt, 0o0755)
                 else:
                     if self.inplace_update:
                         runtime.append(u"--volume=%s:%s:rw" % (
@@ -362,8 +364,10 @@ class DockerCommandLineJob(JobBase):
                         docker_windows_path_adjust(vol.target)))
 
     def run(self, pull_image=True, rm_container=True,
+            record_container_id=False, cidfile_dir="",
+            cidfile_prefix="",
             rm_tmpdir=True, move_outputs="move", **kwargs):
-        # type: (bool, bool, bool, Text, **Any) -> None
+        # type: (bool, bool, bool, Text, Text, bool, Text, **Any) -> None
 
         (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
 
@@ -463,6 +467,26 @@ class DockerCommandLineJob(JobBase):
         # runtime.append("--env=HOME=/tmp")
         runtime.append(u"--env=HOME=%s" % self.builder.outdir)
         
+        # add parameters to docker to write a container ID file
+        if record_container_id:
+            if cidfile_dir != "":
+                if not os.path.isdir(cidfile_dir):
+                    _logger.error("--cidfile-dir %s error:\n%s", cidfile_dir,
+                                  cidfile_dir + " is not a directory or "
+                                  "directory doesn't exist, please check it first")
+                    exit(2)
+                if not os.path.exists(cidfile_dir):
+                    _logger.error("--cidfile-dir %s error:\n%s", cidfile_dir,
+                                  "directory doesn't exist, please create it first")
+                    exit(2)
+            else:
+                cidfile_dir = os.getcwd()
+            cidfile_name = datetime.datetime.now().strftime("%Y%m%d%H%M%S-%f")+".cid"
+            if cidfile_prefix != "":
+                cidfile_name = str(cidfile_prefix + "-" + cidfile_name)
+            cidfile_path = os.path.join(cidfile_dir, cidfile_name)
+            runtime.append(u"--cidfile=%s" % cidfile_path)
+
         for t, v in self.environment.items():
             runtime.append(u"--env=%s=%s" % (t, v))
 
@@ -549,14 +573,14 @@ def _job_popen(
             stdin_path=stdin_path,
         )
         with open(os.path.join(job_dir, "job.json"), "wb") as f:
-            json.dump(job_description, f)
+            json.dump(job_description, codecs.getwriter('utf-8')(f), ensure_ascii=False) # type: ignore
         try:
             job_script = os.path.join(job_dir, "run_job.bash")
             with open(job_script, "wb") as f:
                 f.write(job_script_contents.encode('utf-8'))
             job_run = os.path.join(job_dir, "run_job.py")
             with open(job_run, "wb") as f:
-                f.write(PYTHON_RUN_SCRIPT)
+                f.write(PYTHON_RUN_SCRIPT.encode('utf-8'))
             sp = subprocess.Popen(
                 ["bash", job_script.encode("utf-8")],
                 shell=False,

cwltool/load_tool.py

+"""Loads a CWL document."""
 from __future__ import absolute_import
 # pylint: disable=unused-import
-"""Loads a CWL document."""
 
 import logging
 import os
@@ -9,18 +9,19 @@ import uuid
 import hashlib
 import json
 import copy
-from typing import Any, Callable, Dict, List, Text, Tuple, Union, cast, Iterable
+from typing import (Any, Callable, Dict, Iterable, List, Mapping, Optional,
+        Text, Tuple, Union, cast)
 
 import requests.sessions
 from six import itervalues, string_types
+from six.moves import urllib
 
 import schema_salad.schema as schema
 from avro.schema import Names
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
-from schema_salad.ref_resolver import Fetcher, Loader, file_uri
+from schema_salad.ref_resolver import ContextType, Fetcher, Loader, file_uri
 from schema_salad.sourceline import cmap
 from schema_salad.validate import ValidationException
-from six.moves import urllib
 
 from . import process, update
 from .errors import WorkflowException
@@ -28,7 +29,6 @@ from .process import Process, shortname, get_schema
 from .update import ALLUPDATES
 
 _logger = logging.getLogger("cwltool")
-
 jobloaderctx = {
     u"cwl": "https://w3id.org/cwl/cwl#",
     u"cwltool": "http://commonwl.org/cwltool#",
@@ -36,7 +36,7 @@ jobloaderctx = {
     u"location": {u"@type": u"@id"},
     u"format": {u"@type": u"@id"},
     u"id": u"@id"
-}
+}  # type: ContextType
 
 
 overrides_ctx = {
@@ -45,21 +45,33 @@ overrides_ctx = {
     u"overrides": {
         "@id": "cwltool:overrides",
         "mapSubject": "overrideTarget",
-        "mapPredicate": "override"
     },
-    u"override": {
-        "@id": "cwltool:override",
+    "requirements": {
+        "@id": "https://w3id.org/cwl/cwl#requirements",
         "mapSubject": "class"
     }
-}  # type: Dict[Text, Union[Dict[Any, Any], Text, Iterable[Text]]]
+}  # type: ContextType
+
+
+FetcherConstructorType = Callable[[Dict[Text, Union[Text, bool]],
+    requests.sessions.Session], Fetcher]
+
+loaders = {}  # type: Dict[FetcherConstructorType, Loader]
+
+def default_loader(fetcher_constructor):
+    # type: (Optional[FetcherConstructorType]) -> Loader
+    if fetcher_constructor in loaders:
+        return loaders[fetcher_constructor]
+    else:
+        loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)
+        loaders[fetcher_constructor] = loader
+        return loader
 
 def resolve_tool_uri(argsworkflow,  # type: Text
                      resolver=None,  # type: Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
-                     fetcher_constructor=None,
-                     # type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
+                     fetcher_constructor=None,  # type: FetcherConstructorType
                      document_loader=None  # type: Loader
-):
-    # type: (...) -> Tuple[Text, Text]
+                     ):  # type: (...) -> Tuple[Text, Text]
 
     uri = None  # type: Text
     split = urllib.parse.urlsplit(argsworkflow)
@@ -70,7 +82,7 @@ def resolve_tool_uri(argsworkflow,  # type: Text
         uri = file_uri(str(os.path.abspath(argsworkflow)))
     elif resolver:
         if document_loader is None:
-            document_loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)  # type: ignore
+            document_loader = default_loader(fetcher_constructor)  # type: ignore
         uri = resolver(document_loader, argsworkflow)
 
     if uri is None:
@@ -85,18 +97,17 @@ def resolve_tool_uri(argsworkflow,  # type: Text
 
 def fetch_document(argsworkflow,  # type: Union[Text, Dict[Text, Any]]
                    resolver=None,  # type: Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
-                   fetcher_constructor=None
-                   # type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
-                   ):
-    # type: (...) -> Tuple[Loader, CommentedMap, Text]
+                   fetcher_constructor=None  # type: FetcherConstructorType
+                  ):  # type: (...) -> Tuple[Loader, CommentedMap, Text]
     """Retrieve a CWL document."""
 
-    document_loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)  # type: ignore
+    document_loader = default_loader(fetcher_constructor)  # type: ignore
 
     uri = None  # type: Text
     workflowobj = None  # type: CommentedMap
     if isinstance(argsworkflow, string_types):
-        uri, fileuri = resolve_tool_uri(argsworkflow, resolver=resolver, document_loader=document_loader)
+        uri, fileuri = resolve_tool_uri(argsworkflow, resolver=resolver,
+                document_loader=document_loader)
         workflowobj = document_loader.fetch(fileuri)
     elif isinstance(argsworkflow, dict):
         uri = "#" + Text(id(argsworkflow))
@@ -126,7 +137,7 @@ def _convert_stdstreams_to_files(workflowobj):
                                         sort_keys=True).encode('utf-8')).hexdigest())
                             workflowobj[streamtype] = filename
                         out['type'] = 'File'
-                        out['outputBinding'] = {'glob': filename}
+                        out['outputBinding'] = cmap({'glob': filename})
             for inp in workflowobj.get('inputs', []):
                 if inp.get('type') == 'stdin':
                     if 'inputBinding' in inp:
@@ -170,25 +181,25 @@ def validate_document(document_loader,  # type: Loader
                       enable_dev=False,  # type: bool
                       strict=True,  # type: bool
                       preprocess_only=False,  # type: bool
-                      fetcher_constructor=None,
-                      skip_schemas=None,
-                      # type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
-                      overrides=None  # type: List[Dict]
+                      fetcher_constructor=None,  # type: FetcherConstructorType
+                      skip_schemas=None,  # type: bool
+                      overrides=None,  # type: List[Dict]
+                      metadata=None,  # type: Optional[Dict]
                       ):
     # type: (...) -> Tuple[Loader, Names, Union[Dict[Text, Any], List[Dict[Text, Any]]], Dict[Text, Any], Text]
     """Validate a CWL document."""
 
     if isinstance(workflowobj, list):
-        workflowobj = {
+        workflowobj = cmap({
             "$graph": workflowobj
-        }
+        }, fn=uri)
 
     if not isinstance(workflowobj, dict):
         raise ValueError("workflowjobj must be a dict, got '%s': %s" % (type(workflowobj), workflowobj))
 
     jobobj = None
     if "cwl:tool" in workflowobj:
-        job_loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)  # type: ignore
+        job_loader = default_loader(fetcher_constructor)  # type: ignore
         jobobj, _ = job_loader.resolve_all(workflowobj, uri)
         uri = urllib.parse.urljoin(uri, workflowobj["https://w3id.org/cwl/cwl#tool"])
         del cast(dict, jobobj)["https://w3id.org/cwl/cwl#tool"]
@@ -200,8 +211,14 @@ def validate_document(document_loader,  # type: Loader
         workflowobj = fetch_document(uri, fetcher_constructor=fetcher_constructor)[1]
 
     fileuri = urllib.parse.urldefrag(uri)[0]
+    if "cwlVersion" not in workflowobj:
+        if metadata and 'cwlVersion' in metadata:
+            workflowobj['cwlVersion'] = metadata['cwlVersion']
+        else:
+            raise ValidationException("No cwlVersion found."
+                "Use the following syntax in your CWL document to declare "
+                "the version: cwlVersion: <version>")
 
-    if "cwlVersion" in workflowobj:
     if not isinstance(workflowobj["cwlVersion"], (str, Text)):
         raise Exception("'cwlVersion' must be a string, got %s" % type(workflowobj["cwlVersion"]))
     # strip out version
@@ -213,9 +230,6 @@ def validate_document(document_loader,  # type: Loader
         versions = list(ALLUPDATES)  # ALLUPDATES is a dict
         versions.sort()
         raise ValidationException("'cwlVersion' not valid. Supported CWL versions are: \n{}".format("\n".join(versions)))
-    else:
-        raise ValidationException("No cwlVersion found."
-            "Use the following syntax in your CWL workflow to declare version: cwlVersion: <version>")
 
     if workflowobj["cwlVersion"] == "draft-2":
         workflowobj = cast(CommentedMap, cmap(update._draft2toDraft3dev1(
@@ -238,36 +252,36 @@ def validate_document(document_loader,  # type: Loader
     _add_blank_ids(workflowobj)
 
     workflowobj["id"] = fileuri
-    processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)
+    processobj, new_metadata = document_loader.resolve_all(workflowobj, fileuri)
     if not isinstance(processobj, (CommentedMap, CommentedSeq)):
         raise ValidationException("Workflow must be a dict or list.")
 
-    if not metadata:
+    if not new_metadata:
         if not isinstance(processobj, dict):
             raise ValidationException("Draft-2 workflows must be a dict.")
-        metadata = cast(CommentedMap, cmap({"$namespaces": processobj.get("$namespaces", {}),
+        new_metadata = cast(CommentedMap, cmap(
+            {"$namespaces": processobj.get("$namespaces", {}),
              "$schemas": processobj.get("$schemas", []),
-                                            "cwlVersion": processobj["cwlVersion"]},
-                                           fn=fileuri))
+             "cwlVersion": processobj["cwlVersion"]}, fn=fileuri))
 
     _convert_stdstreams_to_files(workflowobj)
 
     if preprocess_only:
-        return document_loader, avsc_names, processobj, metadata, uri
+        return document_loader, avsc_names, processobj, new_metadata, uri
 
     schema.validate_doc(avsc_names, processobj, document_loader, strict)
 
-    if metadata.get("cwlVersion") != update.LATEST:
+    if new_metadata.get("cwlVersion") != update.LATEST:
         processobj = cast(CommentedMap, cmap(update.update(
-            processobj, document_loader, fileuri, enable_dev, metadata)))
+            processobj, document_loader, fileuri, enable_dev, new_metadata)))
 
     if jobobj:
-        metadata[u"cwl:defaults"] = jobobj
+        new_metadata[u"cwl:defaults"] = jobobj
 
     if overrides:
-        metadata[u"cwltool:overrides"] = overrides
+        new_metadata[u"cwltool:overrides"] = overrides
 
-    return document_loader, avsc_names, processobj, metadata, uri
+    return document_loader, avsc_names, processobj, new_metadata, uri
 
 
 def make_tool(document_loader,  # type: Loader
@@ -322,7 +336,7 @@ def load_tool(argsworkflow,  # type: Union[Text, Dict[Text, Any]]
               enable_dev=False,  # type: bool
               strict=True,  # type: bool
               resolver=None,  # type: Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
-              fetcher_constructor=None,  # type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
+              fetcher_constructor=None,  # type: FetcherConstructorType
               overrides=None
               ):
     # type: (...) -> Process
@@ -332,7 +346,8 @@ def load_tool(argsworkflow,  # type: Union[Text, Dict[Text, Any]]
     document_loader, avsc_names, processobj, metadata, uri = validate_document(
         document_loader, workflowobj, uri, enable_dev=enable_dev,
         strict=strict, fetcher_constructor=fetcher_constructor,
-        overrides=overrides)
+        overrides=overrides, metadata=kwargs.get('metadata', None)
+        if kwargs else None)
     return make_tool(document_loader, avsc_names, metadata, uri,
                      makeTool, kwargs if kwargs else {})
 

cwltool/pack.py

@@ -95,8 +95,8 @@ def import_embed(d, seen):
             import_embed(d[k], seen)
 
 
-def pack(document_loader, processobj, uri, metadata):
-    # type: (Loader, Union[Dict[Text, Any], List[Dict[Text, Any]]], Text, Dict[Text, Text]) -> Dict[Text, Any]
+def pack(document_loader, processobj, uri, metadata, rewrite_out=None):
+    # type: (Loader, Union[Dict[Text, Any], List[Dict[Text, Any]]], Text, Dict[Text, Text], Dict[Text, Text]) -> Dict[Text, Any]
 
     document_loader = SubLoader(document_loader)
     document_loader.idx = {}
@@ -114,15 +114,20 @@ def pack(document_loader, processobj, uri, metadata):
         # type: (Text, Text) -> Union[Dict, List, Text]
         return document_loader.resolve_ref(u, base_url=b)[0]
 
+    ids = set()  # type: Set[Text]
+    find_ids(processobj, ids)
+
     runs = {uri}
     find_run(processobj, loadref, runs)
 
-    ids = set()  # type: Set[Text]
     for f in runs:
         find_ids(document_loader.resolve_ref(f)[0], ids)
 
     names = set()  # type: Set[Text]
+    if rewrite_out is None:
         rewrite = {}  # type: Dict[Text, Text]
+    else:
+        rewrite = rewrite_out
 
     mainpath, _ = urllib.parse.urldefrag(uri)
 
@@ -131,8 +136,10 @@ def pack(document_loader, processobj, uri, metadata):
         if r == mainuri:
             rewrite[r] = "#main"
         elif r.startswith(mainuri) and r[len(mainuri)] in ("#", "/"):
-            path, frag = urllib.parse.urldefrag(r)
-            rewrite[r] = "#"+frag
+            if r[len(mainuri):].startswith("#main/"):
+                rewrite[r] = "#" + uniquename(r[len(mainuri)+1:], names)
+            else:
+                rewrite[r] = "#" + uniquename("main/"+r[len(mainuri)+1:], names)
         else:
             path, frag = urllib.parse.urldefrag(r)
             if path == mainpath:
@@ -144,7 +151,6 @@ def pack(document_loader, processobj, uri, metadata):
     sortedids = sorted(ids)
 
     for r in sortedids:
-        if r in document_loader.idx:
         rewrite_id(r, uri)
 
     packed = {"$graph": [], "cwlVersion": metadata["cwlVersion"]

cwltool/process.py

@@ -422,13 +422,13 @@ def avroize_type(field_type, name_prefix=""):
             avroize_type(field_type["items"], name_prefix)
     return field_type
 
-def get_overrides(overrides, toolid):  # type: (List[Dict[Text, Any]], Text) -> List[Dict[Text, Any]]
-    req = []  # type: List[Dict[Text, Any]]
+def get_overrides(overrides, toolid):  # type: (List[Dict[Text, Any]], Text) -> Dict[Text, Any]
+    req = {}  # type: Dict[Text, Any]
     if not isinstance(overrides, list):
         raise validate.ValidationException("Expected overrides to be a list, but was %s" % type(overrides))
     for ov in overrides:
         if ov["overrideTarget"] == toolid:
-            req.extend(ov["override"])
+            req.update(ov)
     return req
 
 class Process(six.with_metaclass(abc.ABCMeta, object)):
@@ -467,7 +467,7 @@ class Process(six.with_metaclass(abc.ABCMeta, object)):
         self.tool = toolpath_object
         self.requirements = (kwargs.get("requirements", []) +
                              self.tool.get("requirements", []) +
-                             get_overrides(kwargs.get("overrides", []), self.tool["id"]))
+                             get_overrides(kwargs.get("overrides", []), self.tool["id"]).get("requirements", []))
         self.hints = kwargs.get("hints", []) + self.tool.get("hints", [])
         self.formatgraph = None  # type: Graph
         if "loader" in kwargs:
@@ -608,6 +608,7 @@ class Process(six.with_metaclass(abc.ABCMeta, object)):
             builder.stagedir = builder.fs_access.docker_compatible_realpath(kwargs.get("docker_stagedir") or "/var/lib/cwl")
         else:
             builder.outdir = builder.fs_access.realpath(kwargs.get("outdir") or tempfile.mkdtemp())
+            if self.tool[u"class"] != 'Workflow':
                 builder.tmpdir = builder.fs_access.realpath(kwargs.get("tmpdir") or tempfile.mkdtemp())
                 builder.stagedir = builder.fs_access.realpath(kwargs.get("stagedir") or tempfile.mkdtemp())
 

cwltool/workflow.py

@@ -70,11 +70,15 @@ def match_types(sinktype, src, iid, inputobj, linkMerge, valueFrom):
     elif isinstance(src.parameter["type"], list):
         # Source is union type
         # Check that at least one source type is compatible with the sink.
-        for st in src.parameter["type"]:
-            srccopy = copy.deepcopy(src)
-            srccopy.parameter["type"] = st
-            if match_types(sinktype, srccopy, iid, inputobj, linkMerge, valueFrom):
+        original_types = src.parameter["type"]
+        for source_type in original_types:
+            src.parameter["type"] = source_type
+            match = match_types(
+                sinktype, src, iid, inputobj, linkMerge, valueFrom)
+            if match:
+                src.parameter["type"] = original_types
                 return True
+        src.parameter["type"] = original_types
         return False
     elif linkMerge:
         if iid not in inputobj:
@@ -206,13 +210,13 @@ def object_from_state(state, parms, frag_only, supportsMultipleInput, sourceFiel
         if frag_only:
             iid = shortname(iid)
         if sourceField in inp:
-            if (isinstance(inp[sourceField], list) and not
-            supportsMultipleInput):
+            connections = aslist(inp[sourceField])
+            if (len(connections) > 1 and
+                not supportsMultipleInput):
                 raise WorkflowException(
                     "Workflow contains multiple inbound links to a single "
                     "parameter but MultipleInputFeatureRequirement is not "
                     "declared.")
-            connections = aslist(inp[sourceField])
             for src in connections:
                 if src in state and state[src] is not None and (state[src].success == "success" or incomplete):
                     if not match_types(
@@ -669,7 +673,7 @@ class WorkflowStep(Process):
 
         kwargs["requirements"] = (kwargs.get("requirements", []) +
                                   toolpath_object.get("requirements", []) +
-                                  get_overrides(kwargs.get("overrides", []), self.id))
+                                  get_overrides(kwargs.get("overrides", []), self.id).get("requirements", []))
         kwargs["hints"] = kwargs.get("hints", []) + toolpath_object.get("hints", [])
 
         try:
@@ -706,7 +710,14 @@ class WorkflowStep(Process):
                 for tool_entry in self.embedded_tool.tool[toolfield]:
                     frag = shortname(tool_entry["id"])
                     if frag == shortinputid:
+                        #if the case that the step has a default for a parameter,
+                        #we do not want the default of the tool to override it
+                        step_default = None
+                        if "default" in param and "default" in tool_entry:
+                            step_default = param["default"]
                         param.update(tool_entry)
+                        if step_default is not None:
+                            param["default"] = step_default
                         found = True
                         bound.add(frag)
                         break

setup.cfg

@@ -13,6 +13,6 @@ addopts = --ignore cwltool/schemas
 testpaths = tests
 
 [egg_info]
-tag_build = .20171221100033
+tag_build = .20180211183944
 tag_date = 0
 

tests/echo.cwl

+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 inputs:

tests/override/echo-job-ov.yml

 m1: zing
 cwltool:overrides:
   echo.cwl:
-    - class: EnvVarRequirement
+    requirements:
+      EnvVarRequirement:
         envDef:
           MESSAGE: hello3

tests/override/echo-job-ov2.yml

 m1: zing
 cwltool:overrides:
   echo.cwl:
-    - class: EnvVarRequirement
+    requirements:
+      EnvVarRequirement:
         envDef:
           MESSAGE: hello4
 cwl:tool: echo.cwl

tests/override/echo-wf.cwl

+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs:

tests/override/echo.cwl

+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 requirements:
@@ -15,5 +16,5 @@ outputs:
       glob: out.txt
       loadContents: true
       outputEval: $(self[0].contents)
-arguments: ["echo", "-n", $(inputs.m1), {shellQuote: false, valueFrom: "$MESSAGE"}]
+arguments: ["echo", $(inputs.m1), {shellQuote: false, valueFrom: "$MESSAGE"}]
 stdout: out.txt