Merge pull request #202 from common-workflow-language/command-line-re…

…cord-parameters

Command line record parameters

Makefile

@@ -133,7 +133,7 @@ diff-cover.html: coverage-gcovr.xml coverage.xml
 
 ## test        : run the ${MODULE} test suite
 test: FORCE
-	python tests/test_examples.py 
+	./setup.py test
 
 sloccount.sc: ${PYSOURCES} Makefile
 	sloccount --duplicates --wide --details $^ > sloccount.sc

cwltool/main.py

@@ -241,7 +241,6 @@ def output_callback(out, processStatus):
 
     return final_output[0]
 
-
 class FSAction(argparse.Action):
     objclass = None  # type: Text
 
@@ -293,22 +292,15 @@ class FileAppendAction(FSAppendAction):
 class DirectoryAppendAction(FSAppendAction):
     objclass = "Directory"
 
-def generate_parser(toolparser, tool, namemap):
-    # type: (argparse.ArgumentParser, Process, Dict[Text, 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"])
+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 = "--"
 
-        namemap[name.replace("-", "_")] = name
-
-        inptype = inp["type"]
-
         required = True
         if isinstance(inptype, list):
             if inptype[0] == "null":
@@ -319,10 +311,9 @@ def generate_parser(toolparser, tool, namemap):
                     _logger.debug(u"Can't make command line argument from %s", inptype)
                     return None
 
-        ahelp = inp.get("description", "").replace("%", "%%")
+        ahelp = description.replace("%", "%%")
         action = None  # type: Union[argparse.Action, Text]
         atype = None  # type: Any
-        default = None  # type: Any
 
         if inptype == "File":
             action = cast(argparse.Action, FileAction)
@@ -337,6 +328,16 @@ def generate_parser(toolparser, tool, namemap):
                 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":
@@ -348,8 +349,7 @@ def generate_parser(toolparser, tool, namemap):
         elif inptype == "boolean":
             action = "store_true"
 
-        if "default" in inp:
-            default = inp["default"]
+        if default:
             required = False
 
         if not atype and not action:
@@ -365,6 +365,20 @@ def generate_parser(toolparser, tool, namemap):
             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
 
 
@@ -406,12 +420,23 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
     else:
         input_basedir = args.basedir if args.basedir else os.getcwd()
         namemap = {}  # type: Dict[Text, Text]
-        toolparser = generate_parser(argparse.ArgumentParser(prog=args.workflow), t, namemap)
+        records = []  # type: List[Text]
+        toolparser = generate_parser(
+            argparse.ArgumentParser(prog=args.workflow), t, namemap, records)
         if toolparser:
             if args.tool_help:
                 toolparser.print_help()
                 return 0
             cmd_line = vars(toolparser.parse_args(args.job_order))
+            for record_name in records:
+                record = {}
+                record_items = {
+                    k:v for k,v in cmd_line.iteritems()
+                    if k.startswith(record_name)}
+                for key, value in record_items.iteritems():
+                    record[key[len(record_name)+1:]] = value
+                    del cmd_line[key]
+                cmd_line[str(record_name)] = record
 
             if cmd_line["job_order"]:
                 try:

tests/test_toolargparse.py

@@ -42,6 +42,25 @@ class ToolArgparse(unittest.TestCase):
   - echo
   - "ff"
 stdout: foo
+'''
+
+    script3='''
+#!/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: []
 '''
 
     def test_help(self):
@@ -59,3 +78,27 @@ def test_bool(self):
                 self.assertEquals(main([f.name, '--help']), 0)
             except SystemExit as e:
                 self.assertEquals(e.code, 0)
+
+    def test_record_help(self):
+        with NamedTemporaryFile() as f:
+            f.write(self.script3)
+            f.flush()
+            try:
+                self.assertEquals(main([f.name, '--help']), 0)
+            except SystemExit as e:
+                self.assertEquals(e.code, 0)
+
+    def test_record(self):
+        with NamedTemporaryFile() as f:
+            f.write(self.script3)
+            f.flush()
+            try:
+                self.assertEquals(main([f.name, '--foo.one', 'README.rst',
+                '--foo.two', 'test']), 0)
+            except SystemExit as e:
+                self.assertEquals(e.code, 0)
+
+
+
+if __name__ == '__main__':
+    unittest.main()

typeshed/2.7/argparse.pyi

@@ -58,7 +58,8 @@ class ArgumentParser:
                      help: str = ...,
                      metavar: Union[str, Tuple[str, ...]] = ...,
                      dest: str = ...,
-                     version: str = ...) -> None: ...  # weirdly documented
+                     version: str = ...,
+                     **kwargs: Any) -> None: ...  # weirdly documented
     def parse_args(self, args: Optional[Sequence[str]] = ...,
                    namespace: Optional[Namespace] = ...) -> Namespace: ...
     def add_subparsers(self, title: str = ...,
@@ -70,8 +71,8 @@ class ArgumentParser:
                        dest: Optional[str] = ...,
                        help: Optional[str] = ...,
                        metavar: Optional[str] = ...) -> _SubParsersAction: ...
-    def add_argument_group(self, title: Optional[str] = ...,
-                           description: Optional[str] = ...) -> _ArgumentGroup: ...
+    def add_argument_group(self, title: Optional[Text] = ...,
+                           description: Optional[Text] = ...) -> _ArgumentGroup: ...
     def add_mutually_exclusive_group(self, required: bool = ...) -> _MutuallyExclusiveGroup: ...
     def set_defaults(self, **kwargs: Any) -> None: ...
     def get_default(self, dest: str) -> Any: ...

typeshed/2.7/requests/sessions.pyi

@@ -78,7 +78,7 @@ class Session(SessionRedirectMixin):
                 json=...) -> Response: ...
     def get(self, url: AnyStr, **kwargs) -> Response: ...
     def options(self, url: str, **kwargs) -> Response: ...
-    def head(self, url: str, **kwargs) -> Response: ...
+    def head(self, url: AnyStr, **kwargs) -> Response: ...
     def post(self, url: str, data=..., json=..., **kwargs) -> Response: ...
     def put(self, url: str, data=..., **kwargs) -> Response: ...
     def patch(self, url: str, data=..., **kwargs) -> Response: ...