{"repo": "common-workflow-language/cwltool", "pull_number": 95, "instance_id": "common-workflow-language__cwltool-95", "issue_numbers": "", "base_commit": "efc29f3610e7062287037fa9cd834c56397bff62", "patch": "diff --git a/cwltool/builder.py b/cwltool/builder.py\n--- a/cwltool/builder.py\n+++ b/cwltool/builder.py\n@@ -34,9 +34,9 @@ class Builder(object):\n def __init__(self): # type: () -> None\n self.names = None # type: avro.schema.Names\n self.schemaDefs = None # type: Dict[str,Dict[unicode, Any]]\n- self.files = None # type: List[Dict[str, str]]\n+ self.files = None # type: List[Dict[unicode, unicode]]\n self.fs_access = None # type: StdFsAccess\n- self.job = None # type: Dict[str, Any]\n+ self.job = None # type: Dict[unicode, Union[Dict[unicode, Any], List, unicode]]\n self.requirements = None # type: List[Dict[str,Any]]\n self.outdir = None # type: str\n self.tmpdir = None # type: str\ndiff --git a/cwltool/cwlrdf.py b/cwltool/cwlrdf.py\n--- a/cwltool/cwlrdf.py\n+++ b/cwltool/cwlrdf.py\n@@ -6,7 +6,7 @@\n from typing import Any, Union, Dict, IO\n \n def makerdf(workflow, wf, ctx):\n- # type: (Union[str, unicode], Dict[str,Any], Loader.ContextType) -> Graph\n+ # type: (Union[str, unicode], Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader.ContextType) -> Graph\n prefixes = {}\n for k,v in ctx.iteritems():\n if isinstance(v, dict):\n@@ -18,7 +18,11 @@ def makerdf(workflow, wf, ctx):\n p, _ = frg.split(\"/\")\n prefixes[p] = u\"%s#%s/\" % (doc_url, p)\n \n- wf[\"@context\"] = ctx\n+ if isinstance(wf, list):\n+ for entry in wf:\n+ entry[\"@context\"] = ctx\n+ else:\n+ wf[\"@context\"] = ctx\n g = Graph().parse(data=json.dumps(wf), format='json-ld', location=workflow)\n \n # Bug in json-ld loader causes @id fields to be added to the graph\n@@ -31,7 +35,7 @@ def makerdf(workflow, wf, ctx):\n return g\n \n def printrdf(workflow, wf, ctx, sr, stdout):\n- # type: (Union[str, unicode], Dict[str, Any], Loader.ContextType, str, IO[Any]) -> None\n+ # type: (Union[str, unicode], Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader.ContextType, str, IO[Any]) -> None\n stdout.write(makerdf(workflow, wf, ctx).serialize(format=sr))\n \n def lastpart(uri): # type: (Any) -> str\n@@ -172,7 +176,7 @@ def dot_without_parameters(g, stdout): # type: (Graph, IO[Any]) -> None\n \n \n def printdot(workflow, wf, ctx, stdout, include_parameters=False):\n- # type: (Union[str, unicode], Dict[str, Any], Loader.ContextType, Any, bool) -> None\n+ # type: (Union[str, unicode], Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader.ContextType, Any, bool) -> None\n g = makerdf(workflow, wf, ctx)\n \n stdout.write(\"digraph {\")\ndiff --git a/cwltool/draft2tool.py b/cwltool/draft2tool.py\n--- a/cwltool/draft2tool.py\n+++ b/cwltool/draft2tool.py\n@@ -30,7 +30,7 @@\n \n class ExpressionTool(Process):\n def __init__(self, toolpath_object, **kwargs):\n- # type: (Dict[str,List[None]], **Any) -> None\n+ # type: (Dict[unicode, Any], **Any) -> None\n super(ExpressionTool, self).__init__(toolpath_object, **kwargs)\n \n class ExpressionJob(object):\n@@ -53,7 +53,7 @@ def run(self, **kwargs): # type: (**Any) -> None\n self.output_callback({}, \"permanentFail\")\n \n def job(self, joborder, output_callback, **kwargs):\n- # type: (Dict[str,str], str, Callable[[Any, Any], Any], **Any) -> Generator[ExpressionTool.ExpressionJob, None, None]\n+ # type: (Dict[unicode, unicode], Callable[[Any, Any], Any], **Any) -> Generator[ExpressionTool.ExpressionJob, None, None]\n builder = self._init_job(joborder, **kwargs)\n \n j = ExpressionTool.ExpressionJob()\n@@ -113,14 +113,14 @@ def run(self, **kwargs):\n \n class CommandLineTool(Process):\n def __init__(self, toolpath_object, **kwargs):\n- # type: (Dict[str,Any], **Any) -> None\n+ # type: (Dict[unicode, Any], **Any) -> None\n super(CommandLineTool, self).__init__(toolpath_object, **kwargs)\n \n def makeJobRunner(self): # type: () -> CommandLineJob\n return CommandLineJob()\n \n def makePathMapper(self, reffiles, **kwargs):\n- # type: (Set[str], str, **Any) -> PathMapper\n+ # type: (Set[unicode], **Any) -> PathMapper\n dockerReq, _ = self.get_requirement(\"DockerRequirement\")\n try:\n if dockerReq and kwargs.get(\"use_container\"):\n@@ -132,7 +132,7 @@ def makePathMapper(self, reffiles, **kwargs):\n raise WorkflowException(u\"Missing input file %s\" % e)\n \n def job(self, joborder, output_callback, **kwargs):\n- # type: (Dict[str,str], str, Callable[..., Any], **Any) -> Generator[Union[CommandLineJob, CallbackJob], None, None]\n+ # type: (Dict[unicode, unicode], Callable[..., Any], **Any) -> Generator[Union[CommandLineJob, CallbackJob], None, None]\n \n jobname = uniquename(kwargs.get(\"name\", shortname(self.tool.get(\"id\", \"job\"))))\n \n@@ -149,7 +149,7 @@ def job(self, joborder, output_callback, **kwargs):\n if docker_req and kwargs.get(\"use_container\") is not False:\n dockerimg = docker_req.get(\"dockerImageId\") or docker_req.get(\"dockerPull\")\n cmdline = [\"docker\", \"run\", dockerimg] + cmdline\n- keydict = {\"cmdline\": cmdline}\n+ keydict = {u\"cmdline\": cmdline}\n \n for _,f in cachebuilder.pathmapper.items():\n st = os.stat(f[0])\n@@ -200,7 +200,7 @@ def rm_pending_output_callback(output_callback, jobcachepending,\n \n builder = self._init_job(joborder, **kwargs)\n \n- reffiles = set((f[\"path\"] for f in builder.files))\n+ reffiles = set((f[u\"path\"] for f in builder.files))\n \n j = self.makeJobRunner()\n j.builder = builder\n@@ -292,9 +292,9 @@ def _check_adjust(f): # type: (Dict[str,Any]) -> Dict[str,Any]\n yield j\n \n def collect_output_ports(self, ports, builder, outdir):\n- # type: (Set[Dict[str,Any]], Builder, str) -> Dict[str,Union[str,List[Any],Dict[str,Any]]]\n+ # type: (Set[Dict[str,Any]], Builder, str) -> Dict[unicode, Union[unicode, List[Any], Dict[unicode, Any]]]\n try:\n- ret = {} # type: Dict[str,Union[str,List[Any],Dict[str,Any]]]\n+ ret = {} # type: Dict[unicode, Union[unicode, List[Any], Dict[unicode, Any]]]\n custom_output = os.path.join(outdir, \"cwl.output.json\")\n if builder.fs_access.exists(custom_output):\n with builder.fs_access.open(custom_output, \"r\") as f:\n@@ -323,7 +323,7 @@ def collect_output_ports(self, ports, builder, outdir):\n raise WorkflowException(\"Error validating output record, \" + str(e) + \"\\n in \" + json.dumps(ret, indent=4))\n \n def collect_output(self, schema, builder, outdir):\n- # type: (Dict[str,Any], Builder, str) -> Union[Dict[str, Any], List[Union[Dict[str, Any], str]]]\n+ # type: (Dict[str,Any], Builder, str) -> Union[Dict[unicode, Any], List[Union[Dict[unicode, Any], unicode]]]\n r = [] # type: List[Any]\n if \"outputBinding\" in schema:\n binding = schema[\"outputBinding\"]\ndiff --git a/cwltool/expression.py b/cwltool/expression.py\n--- a/cwltool/expression.py\n+++ b/cwltool/expression.py\n@@ -19,7 +19,7 @@ def jshead(engineConfig, rootvars):\n return u\"\\n\".join(engineConfig + [u\"var %s = %s;\" % (k, json.dumps(v, indent=4)) for k, v in rootvars.items()])\n \n def exeval(ex, jobinput, requirements, outdir, tmpdir, context, pull_image):\n- # type: (Dict[str,Any], Dict[str,str], List[Dict[str, Any]], str, str, Any, bool) -> sandboxjs.JSON\n+ # type: (Dict[str, Any], Dict[unicode, Union[Dict, List, unicode]], List[Dict[str, Any]], str, str, Any, bool) -> sandboxjs.JSON\n \n if ex[\"engine\"] == \"https://w3id.org/cwl/cwl#JavascriptEngine\":\n engineConfig = [] # type: List[unicode]\n@@ -126,7 +126,7 @@ def param_interpolate(ex, obj, strip=True):\n \n def do_eval(ex, jobinput, requirements, outdir, tmpdir, resources,\n context=None, pull_image=True, timeout=None):\n- # type: (Any, Dict[str,str], List[Dict[str,Any]], str, str, Dict[str, Union[int, str]], Any, bool, int) -> Any\n+ # type: (Union[dict, unicode], Dict[unicode, Union[Dict, List, unicode]], List[Dict[str, Any]], str, str, Dict[str, Union[int, str]], Any, bool, int) -> Any\n \n runtime = resources.copy()\n runtime[\"tmpdir\"] = tmpdir\n@@ -140,7 +140,7 @@ def do_eval(ex, jobinput, requirements, outdir, tmpdir, resources,\n \n if isinstance(ex, dict) and \"engine\" in ex and \"script\" in ex:\n return exeval(ex, jobinput, requirements, outdir, tmpdir, context, pull_image)\n- if isinstance(ex, basestring):\n+ if isinstance(ex, (str, unicode)):\n for r in requirements:\n if r[\"class\"] == \"InlineJavascriptRequirement\":\n return sandboxjs.interpolate(str(ex), jshead(r.get(\"expressionLib\", []), rootvars),\ndiff --git a/cwltool/job.py b/cwltool/job.py\n--- a/cwltool/job.py\n+++ b/cwltool/job.py\n@@ -42,7 +42,7 @@ class CommandLineJob(object):\n \n def __init__(self): # type: () -> None\n self.builder = None # type: Builder\n- self.joborder = None # type: Dict[str,str]\n+ self.joborder = None # type: Dict[unicode, Union[Dict[unicode, Any], List, unicode]]\n self.stdin = None # type: str\n self.stdout = None # type: str\n self.successCodes = None # type: Iterable[int]\ndiff --git a/cwltool/load_tool.py b/cwltool/load_tool.py\n--- a/cwltool/load_tool.py\n+++ b/cwltool/load_tool.py\n@@ -44,7 +44,7 @@ def fetch_document(argsworkflow):\n \n def validate_document(document_loader, workflowobj, uri,\n enable_dev=False, strict=True, preprocess_only=False):\n- # type: (Loader, Dict[unicode, Any], unicode, bool, bool, bool) -> Tuple[Loader, Names, Any, Dict[str, str], unicode]\n+ # type: (Loader, Dict[unicode, Any], unicode, bool, bool, bool) -> Tuple[Loader, Names, Union[Dict[unicode, Any], List[Dict[unicode, Any]]], Dict[unicode, Any], unicode]\n \"\"\"Validate a CWL document.\"\"\"\n jobobj = None\n if \"cwl:tool\" in workflowobj:\n@@ -83,8 +83,13 @@ def validate_document(document_loader, workflowobj, uri,\n \n workflowobj[\"id\"] = fileuri\n processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)\n+ if not isinstance(processobj, (dict, list)):\n+ raise validate.ValidationException(\"Workflow must be a dict or list.\")\n \n if not metadata:\n+ if not isinstance(processobj, dict):\n+ raise validate.ValidationException(\n+ \"Draft-2 workflows must be a dict.\")\n metadata = {\"$namespaces\": processobj.get(\"$namespaces\", {}),\n \"$schemas\": processobj.get(\"$schemas\", []),\n \"cwlVersion\": processobj[\"cwlVersion\"]}\n@@ -92,7 +97,6 @@ def validate_document(document_loader, workflowobj, uri,\n if preprocess_only:\n return document_loader, avsc_names, processobj, metadata, uri\n \n- document_loader.validate_links(processobj)\n schema.validate_doc(avsc_names, processobj, document_loader, strict)\n \n if metadata.get(\"cwlVersion\") != update.LATEST:\n@@ -100,14 +104,13 @@ def validate_document(document_loader, workflowobj, uri,\n processobj, document_loader, fileuri, enable_dev, metadata)\n \n if jobobj:\n- metadata[\"cwl:defaults\"] = jobobj\n+ metadata[u\"cwl:defaults\"] = jobobj\n \n return document_loader, avsc_names, processobj, metadata, uri\n \n \n-def make_tool(document_loader, avsc_names, processobj, metadata, uri, makeTool,\n- kwargs):\n- # type: (Loader, Names, Dict[str, Any], Dict[str, Any], unicode, Callable[..., Process], Dict[str, Any]) -> Process\n+def make_tool(document_loader, avsc_names, metadata, uri, makeTool, kwargs):\n+ # type: (Loader, Names, Dict[unicode, Any], unicode, Callable[..., Process], Dict[str, Any]) -> Process\n \"\"\"Make a Python CWL object.\"\"\"\n resolveduri = document_loader.resolve_ref(uri)[0]\n \n@@ -121,7 +124,7 @@ def make_tool(document_loader, avsc_names, processobj, metadata, uri, makeTool,\n urlparse.urldefrag(i[\"id\"])[1] for i in resolveduri\n if \"id\" in i))\n else:\n- processobj = cast(Dict[str, Any], resolveduri)\n+ processobj = resolveduri\n \n kwargs = kwargs.copy()\n kwargs.update({\n@@ -149,5 +152,5 @@ def load_tool(argsworkflow, makeTool, kwargs=None,\n document_loader, avsc_names, processobj, metadata, uri = validate_document(\n document_loader, workflowobj, uri, enable_dev=enable_dev,\n strict=strict)\n- return make_tool(document_loader, avsc_names, processobj, metadata, uri,\n+ return make_tool(document_loader, avsc_names, metadata, uri,\n makeTool, kwargs if kwargs else {})\ndiff --git a/cwltool/main.py b/cwltool/main.py\n--- a/cwltool/main.py\n+++ b/cwltool/main.py\n@@ -152,7 +152,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser\n \n \n def single_job_executor(t, job_order_object, **kwargs):\n- # type: (Process, Dict[str,Any], str, argparse.Namespace,**Any) -> Union[str,Dict[str,str]]\n+ # type: (Process, Dict[unicode, Any], **Any) -> Union[str,Dict[str,str]]\n final_output = []\n final_status = []\n \n@@ -238,7 +238,7 @@ def __call__(self, parser, namespace, values, option_string=None):\n \n \n def generate_parser(toolparser, tool, namemap):\n- # type: (argparse.ArgumentParser, Process,Dict[str,str]) -> argparse.ArgumentParser\n+ # type: (argparse.ArgumentParser, Process, Dict[unicode, unicode]) -> argparse.ArgumentParser\n toolparser.add_argument(\"job_order\", nargs=\"?\", help=\"Job input json file\")\n namemap[\"job_order\"] = \"job_order\"\n \n@@ -298,14 +298,15 @@ def generate_parser(toolparser, tool, namemap):\n else:\n typekw = {}\n \n- toolparser.add_argument(flag + name, required=required,\n- help=ahelp, action=action, default=default, **typekw)\n+ toolparser.add_argument( # type: ignore\n+ args=flag + name, required=required, help=ahelp, action=action,\n+ default=default, **typekw)\n \n return toolparser\n \n \n def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False, stdout=sys.stdout):\n- # type: (argparse.Namespace, Process, argparse.ArgumentParser, IO[Any], bool, bool, IO[Any]) -> Union[int,Tuple[Dict[str,Any],str]]\n+ # type: (argparse.Namespace, Process, IO[Any], bool, bool, IO[Any]) -> Union[int,Tuple[Dict[str,Any],str]]\n \n job_order_object = None\n \n@@ -313,9 +314,9 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,\n loader = Loader({})\n else:\n jobloaderctx = {\n- \"path\": {\"@type\": \"@id\"},\n- \"format\": {\"@type\": \"@id\"},\n- \"id\": \"@id\"}\n+ u\"path\": {u\"@type\": u\"@id\"},\n+ u\"format\": {u\"@type\": u\"@id\"},\n+ u\"id\": u\"@id\"}\n jobloaderctx.update(t.metadata.get(\"$namespaces\", {}))\n loader = Loader(jobloaderctx)\n \n@@ -332,14 +333,14 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,\n elif job_order_file:\n input_basedir = args.basedir if args.basedir else os.path.abspath(os.path.dirname(job_order_file))\n try:\n- job_order_object, _ = loader.resolve_ref(job_order_file)\n+ job_order_object, _ = loader.resolve_ref(job_order_file, checklinks=False)\n except Exception as e:\n _logger.error(str(e), exc_info=(e if args.debug else False))\n return 1\n toolparser = None\n else:\n input_basedir = args.basedir if args.basedir else os.getcwd()\n- namemap = {} # type: Dict[str,str]\n+ namemap = {} # type: Dict[unicode, unicode]\n toolparser = generate_parser(argparse.ArgumentParser(prog=args.workflow), t, namemap)\n if toolparser:\n if args.tool_help:\n@@ -419,7 +420,7 @@ def makeRelative(u):\n \n stdout.write(json.dumps(deps, indent=4))\n \n-def flatten_deps(d, files):\n+def flatten_deps(d, files): # type: (Any, Set[unicode]) -> None\n if isinstance(d, list):\n for s in d:\n flatten_deps(s, files)\n@@ -428,33 +429,36 @@ def flatten_deps(d, files):\n if \"secondaryFiles\" in d:\n flatten_deps(d[\"secondaryFiles\"], files)\n \n-def find_run(d, runs):\n+def find_run(d, runs): # type: (Any, Set[unicode]) -> None\n if isinstance(d, list):\n for s in d:\n find_run(s, runs)\n elif isinstance(d, dict):\n- if \"run\" in d and isinstance(d[\"run\"], basestring):\n+ if \"run\" in d and isinstance(d[\"run\"], (str, unicode)):\n runs.add(d[\"run\"])\n for s in d.values():\n find_run(s, runs)\n \n def replace_refs(d, rewrite, stem, newstem):\n+ # type: (Any, Dict[unicode, unicode], unicode, unicode) -> None\n if isinstance(d, list):\n for s,v in enumerate(d):\n- if isinstance(v, basestring) and v.startswith(stem):\n+ if isinstance(v, (str, unicode)) and v.startswith(stem):\n d[s] = newstem + v[len(stem):]\n else:\n replace_refs(v, rewrite, stem, newstem)\n elif isinstance(d, dict):\n- if \"run\" in d and isinstance(d[\"run\"], basestring):\n+ if \"run\" in d and isinstance(d[\"run\"], (str, unicode)):\n d[\"run\"] = rewrite[d[\"run\"]]\n for s,v in d.items():\n- if isinstance(v, basestring) and v.startswith(stem):\n+ if isinstance(v, (str, unicode)) and v.startswith(stem):\n d[s] = newstem + v[len(stem):]\n replace_refs(v, rewrite, stem, newstem)\n \n def print_pack(document_loader, processobj, uri, metadata):\n+ # type: (Loader, Any, unicode, Dict[unicode, unicode]) -> str\n def loadref(b, u):\n+ # type: (unicode, unicode) -> Union[Dict, List, unicode]\n return document_loader.resolve_ref(u, base_url=b)[0]\n deps = process.scandeps(uri, processobj,\n set((\"run\",)), set(), loadref)\n@@ -462,7 +466,7 @@ def loadref(b, u):\n fdeps = set((uri,))\n flatten_deps(deps, fdeps)\n \n- runs = set()\n+ runs = set() # type: Set[unicode]\n for f in fdeps:\n find_run(document_loader.idx[f], runs)\n \n@@ -476,9 +480,10 @@ def loadref(b, u):\n for r in runs:\n rewrite[r] = \"#\" + shortname(r)\n \n- packed = {\"$graph\": [], \"cwlVersion\": metadata[\"cwlVersion\"]}\n+ packed = {\"$graph\": [], \"cwlVersion\": metadata[\"cwlVersion\"]\n+ } # type: Dict[unicode, Any]\n for r,v in rewrite.items():\n- dc = copy.deepcopy(document_loader.idx[r])\n+ dc = cast(Dict[unicode, Any], copy.deepcopy(document_loader.idx[r]))\n dc[\"id\"] = v\n dc[\"name\"] = v\n replace_refs(dc, rewrite, r+\"/\" if \"#\" in r else r+\"#\", v+\"/\")\n@@ -508,7 +513,7 @@ def main(argsl=None,\n stderr=sys.stderr,\n versionfunc=versionstring,\n job_order_object=None):\n- # type: (List[str],Callable[...,Union[str,Dict[str,str]]],Callable[...,Process],Callable[[Dict[str,int]],Dict[str,int]],argparse.ArgumentParser,IO[Any],IO[Any],IO[Any],Callable[[],unicode]) -> int\n+ # type: (List[str], argparse.Namespace, Callable[..., Union[str, Dict[str, str]]], Callable[..., Process], Callable[[Dict[str, int]], Dict[str, int]], IO[Any], IO[Any], IO[Any], Callable[[], unicode], Union[int, Tuple[Dict[str, Any], str]]) -> int\n \n _logger.removeHandler(defaultStreamHandler)\n stderr_handler = logging.StreamHandler(stderr)\n@@ -588,8 +593,8 @@ def main(argsl=None,\n printdot(uri, processobj, document_loader.ctx, stdout)\n return 0\n \n- tool = make_tool(document_loader, avsc_names, processobj, metadata,\n- uri, makeTool, {})\n+ tool = make_tool(document_loader, avsc_names, metadata, uri,\n+ makeTool, {})\n except (validate.ValidationException) as exc:\n _logger.error(u\"Tool definition failed validation:\\n%s\", exc,\n exc_info=(exc if args.debug else False))\n@@ -611,14 +616,15 @@ def main(argsl=None,\n \n if args.tmp_outdir_prefix != 'tmp':\n # Use user defined temp directory (if it exists)\n- args.tmp_outdir_prefix = os.path.abspath(args.tmp_outdir_prefix)\n+ setattr(args, 'tmp_outdir_prefix',\n+ os.path.abspath(args.tmp_outdir_prefix))\n if not os.path.exists(args.tmp_outdir_prefix):\n _logger.error(\"Intermediate output directory prefix doesn't exist.\")\n return 1\n \n if args.tmpdir_prefix != 'tmp':\n # Use user defined prefix (if the folder exists)\n- args.tmpdir_prefix = os.path.abspath(args.tmpdir_prefix)\n+ setattr(args, 'tmpdir_prefix', os.path.abspath(args.tmpdir_prefix))\n if not os.path.exists(args.tmpdir_prefix):\n _logger.error(\"Temporary directory prefix doesn't exist.\")\n return 1\n@@ -633,12 +639,13 @@ def main(argsl=None,\n return job_order_object\n \n if args.cachedir:\n- args.cachedir = os.path.abspath(args.cachedir)\n- args.move_outputs = False\n+ setattr(args, 'cachedir', os.path.abspath(args.cachedir))\n+ setattr(args, 'move_outputs', False)\n \n try:\n- args.tmp_outdir_prefix = args.cachedir if args.cachedir else args.tmp_outdir_prefix\n- args.basedir = job_order_object[1]\n+ setattr(args, 'tmp_outdir_prefix',\n+ args.cachedir if args.cachedir else args.tmp_outdir_prefix)\n+ setattr(args, 'basedir', job_order_object[1])\n del args.workflow\n del args.job_order\n out = executor(tool, job_order_object[0],\ndiff --git a/cwltool/pathmapper.py b/cwltool/pathmapper.py\n--- a/cwltool/pathmapper.py\n+++ b/cwltool/pathmapper.py\n@@ -7,8 +7,8 @@\n _logger = logging.getLogger(\"cwltool\")\n \n \n-def abspath(src, basedir): # type: (str,str) -> str\n- if src.startswith(\"file://\"):\n+def abspath(src, basedir): # type: (unicode, unicode) -> unicode\n+ if src.startswith(u\"file://\"):\n ab = src[7:]\n else:\n ab = src if os.path.isabs(src) else os.path.join(basedir, src)\n@@ -21,31 +21,31 @@ class PathMapper(object):\n (absolute local path, absolute container path)\"\"\"\n \n def __init__(self, referenced_files, basedir):\n- # type: (Set[str], str) -> None\n- self._pathmap = {} # type: Dict[str, Tuple[str, str]]\n+ # type: (Set[unicode], unicode) -> None\n+ self._pathmap = {} # type: Dict[unicode, Tuple[unicode, unicode]]\n self.setup(referenced_files, basedir)\n \n def setup(self, referenced_files, basedir):\n- # type: (Set[str], str) -> None\n+ # type: (Set[unicode], unicode) -> None\n for src in referenced_files:\n ab = abspath(src, basedir)\n self._pathmap[src] = (ab, ab)\n \n- def mapper(self, src): # type: (str) -> Tuple[str,str]\n- if \"#\" in src:\n- i = src.index(\"#\")\n+ def mapper(self, src): # type: (unicode) -> Tuple[unicode, unicode]\n+ if u\"#\" in src:\n+ i = src.index(u\"#\")\n p = self._pathmap[src[:i]]\n return (p[0], p[1] + src[i:])\n else:\n return self._pathmap[src]\n \n- def files(self): # type: () -> List[str]\n+ def files(self): # type: () -> List[unicode]\n return self._pathmap.keys()\n \n- def items(self): # type: () -> List[Tuple[str,Tuple[str,str]]]\n+ def items(self): # type: () -> List[Tuple[unicode, Tuple[unicode, unicode]]]\n return self._pathmap.items()\n \n- def reversemap(self, target): # type: (str) -> Tuple[str, str]\n+ def reversemap(self, target): # type: (unicode) -> Tuple[unicode, unicode]\n for k, v in self._pathmap.items():\n if v[1] == target:\n return (k, v[0])\n@@ -55,8 +55,8 @@ def reversemap(self, target): # type: (str) -> Tuple[str, str]\n class DockerPathMapper(PathMapper):\n \n def __init__(self, referenced_files, basedir):\n- # type: (Set[str], str) -> None\n- self.dirs = {} # type: Dict[str, Union[bool, str]]\n+ # type: (Set[unicode], unicode) -> None\n+ self.dirs = {} # type: Dict[unicode, Union[bool, unicode]]\n super(DockerPathMapper, self).__init__(referenced_files, basedir)\n \n def setup(self, referenced_files, basedir):\n@@ -77,16 +77,16 @@ def setup(self, referenced_files, basedir):\n del self.dirs[d]\n self.dirs[dirn] = True\n \n- prefix = \"job\" + str(random.randint(1, 1000000000)) + \"_\"\n+ prefix = u\"job\" + str(random.randint(1, 1000000000)) + u\"_\"\n \n- names = set() # type: Set[str]\n+ names = set() # type: Set[unicode]\n for d in self.dirs:\n- name = os.path.join(\"/var/lib/cwl\", prefix + os.path.basename(d))\n+ name = os.path.join(u\"/var/lib/cwl\", prefix + os.path.basename(d))\n i = 1\n while name in names:\n i += 1\n- name = os.path.join(\"/var/lib/cwl\",\n- prefix + os.path.basename(d) + str(i))\n+ name = os.path.join(u\"/var/lib/cwl\",\n+ prefix + os.path.basename(d) + unicode(i))\n names.add(name)\n self.dirs[d] = name\n \ndiff --git a/cwltool/process.py b/cwltool/process.py\n--- a/cwltool/process.py\n+++ b/cwltool/process.py\n@@ -20,7 +20,8 @@\n import glob\n from .errors import WorkflowException\n from .pathmapper import abspath\n-from typing import Any, Callable, Generator, Union, IO, AnyStr, Tuple\n+from typing import (Any, AnyStr, Callable, cast, Dict, List, Generator, IO,\n+ Tuple, Union)\n from collections import Iterable\n from rdflib import URIRef\n from rdflib.namespace import RDFS, OWL\n@@ -52,6 +53,7 @@\n \"invocation.md\")\n \n salad_files = ('metaschema.yml',\n+ 'metaschema_base.yml',\n 'salad.md',\n 'field_name.yml',\n 'import_include.md',\n@@ -72,9 +74,9 @@\n 'vocab_res_src.yml',\n 'vocab_res_proc.yml')\n \n-SCHEMA_CACHE = {} # type: Dict[str, Tuple[Loader, Union[avro.schema.Names, avro.schema.SchemaParseException], Dict[unicode,Any], Loader]]\n-SCHEMA_FILE = None\n-SCHEMA_ANY = None\n+SCHEMA_CACHE = {} # type: Dict[str, Tuple[Loader, Union[avro.schema.Names, avro.schema.SchemaParseException], Dict[unicode, Any], Loader]]\n+SCHEMA_FILE = None # type: Dict[unicode, Any]\n+SCHEMA_ANY = None # type: Dict[unicode, Any]\n \n def get_schema(version):\n # type: (str) -> Tuple[Loader, Union[avro.schema.Names, avro.schema.SchemaParseException], Dict[unicode,Any], Loader]\n@@ -107,18 +109,20 @@ def get_schema(version):\n \"https://w3id.org/cwl/CommonWorkflowLanguage.yml\", cache=cache)\n \n global SCHEMA_FILE, SCHEMA_ANY # pylint: disable=global-statement\n- SCHEMA_FILE = SCHEMA_CACHE[version][3].idx[\"https://w3id.org/cwl/cwl#File\"]\n- SCHEMA_ANY = SCHEMA_CACHE[version][3].idx[\"https://w3id.org/cwl/salad#Any\"]\n+ SCHEMA_FILE = cast(Dict[unicode, Any],\n+ SCHEMA_CACHE[version][3].idx[\"https://w3id.org/cwl/cwl#File\"])\n+ SCHEMA_ANY = cast(Dict[unicode, Any],\n+ SCHEMA_CACHE[version][3].idx[\"https://w3id.org/cwl/salad#Any\"])\n \n return SCHEMA_CACHE[version]\n \n def shortname(inputid):\n- # type: (Union[str, unicode]) -> str\n+ # type: (unicode) -> unicode\n d = urlparse.urlparse(inputid)\n if d.fragment:\n- return d.fragment.split(\"/\")[-1].split(\".\")[-1]\n+ return d.fragment.split(u\"/\")[-1].split(u\".\")[-1]\n else:\n- return d.path.split(\"/\")[-1]\n+ return d.path.split(u\"/\")[-1]\n \n \n class UnsupportedRequirement(Exception):\n@@ -202,7 +206,7 @@ def formatSubclassOf(fmt, cls, ontology, visited):\n \n \n def checkFormat(actualFile, inputFormats, ontology):\n- # type: (Union[Dict[str, Any], List[Dict[str, Any]]], Any, Graph) -> None\n+ # type: (Union[Dict[unicode, Any], List, unicode], Union[List[unicode], unicode], Graph) -> None\n for af in aslist(actualFile):\n if \"format\" not in af:\n raise validate.ValidationException(u\"Missing required 'format' for File %s\" % af)\n@@ -212,13 +216,13 @@ def checkFormat(actualFile, inputFormats, ontology):\n raise validate.ValidationException(u\"Incompatible file format %s required format(s) %s\" % (af[\"format\"], inputFormats))\n \n def fillInDefaults(inputs, job):\n- # type: (List[Dict[str, str]], Dict[str, str]) -> None\n+ # type: (List[Dict[unicode, unicode]], Dict[unicode, Union[Dict[unicode, Any], List, unicode]]) -> None\n for inp in inputs:\n- if shortname(inp[\"id\"]) in job:\n+ if shortname(inp[u\"id\"]) in job:\n pass\n- elif shortname(inp[\"id\"]) not in job and \"default\" in inp:\n- job[shortname(inp[\"id\"])] = copy.copy(inp[\"default\"])\n- elif shortname(inp[\"id\"]) not in job and inp[\"type\"][0] == \"null\":\n+ elif shortname(inp[u\"id\"]) not in job and u\"default\" in inp:\n+ job[shortname(inp[u\"id\"])] = copy.copy(inp[u\"default\"])\n+ elif shortname(inp[u\"id\"]) not in job and inp[u\"type\"][0] == u\"null\":\n pass\n else:\n raise validate.ValidationException(\"Missing input parameter `%s`\" % shortname(inp[\"id\"]))\n@@ -227,7 +231,7 @@ class Process(object):\n __metaclass__ = abc.ABCMeta\n \n def __init__(self, toolpath_object, **kwargs):\n- # type: (Dict[str, Any], **Any) -> None\n+ # type: (Dict[unicode, Any], **Any) -> None\n self.metadata = kwargs.get(\"metadata\", {}) # type: Dict[str,Any]\n self.names = None # type: avro.schema.Names\n names = schema_salad.schema.make_avro_schema(\n@@ -298,11 +302,12 @@ def __init__(self, toolpath_object, **kwargs):\n \n \n def _init_job(self, joborder, **kwargs):\n- # type: (Dict[str, str], str, **Any) -> Builder\n+ # type: (Dict[unicode, unicode], **Any) -> Builder\n builder = Builder()\n- builder.job = copy.deepcopy(joborder)\n+ builder.job = cast(Dict[unicode, Union[Dict[unicode, Any], List,\n+ unicode]], copy.deepcopy(joborder))\n \n- fillInDefaults(self.tool[\"inputs\"], builder.job)\n+ fillInDefaults(self.tool[u\"inputs\"], builder.job)\n \n # Validate job order\n try:\n@@ -427,7 +432,7 @@ def visit(self, op):\n \n @abc.abstractmethod\n def job(self, job_order, output_callbacks, **kwargs):\n- # type: (Dict[str, str], str, Callable[[Any, Any], Any], **Any) -> Generator[Any, None, None]\n+ # type: (Dict[unicode, unicode], Callable[[Any, Any], Any], **Any) -> Generator[Any, None, None]\n return None\n \n def empty_subtree(dirpath): # type: (AnyStr) -> bool\n@@ -461,7 +466,7 @@ def uniquename(stem): # type: (unicode) -> unicode\n return u\n \n def scandeps(base, doc, reffields, urlfields, loadref):\n- # type: (str, Any, Set[str], Set[str], Callable[[str, str], Any]) -> List[Dict[str, str]]\n+ # type: (unicode, Any, Set[str], Set[str], Callable[[unicode, str], Any]) -> List[Dict[str, str]]\n r = []\n if isinstance(doc, dict):\n if \"id\" in doc:\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/__init__.py b/cwltool/schemas/draft-4/salad/schema_salad/__init__.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/__init__.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/__init__.py\n@@ -1,7 +1,6 @@\n import logging\n import sys\n-if sys.version_info >= (2,7):\n- import typing\n+import typing\n \n __author__ = 'peter.amstutz@curoverse.com'\n \ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/__main__.py b/cwltool/schemas/draft-4/salad/schema_salad/__main__.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/__main__.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/__main__.py\n@@ -1,6 +1,5 @@\n from . import main\n import sys\n-if sys.version_info >= (2,7):\n- import typing\n+import typing\n \n sys.exit(main.main())\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/add_dictlist.py b/cwltool/schemas/draft-4/salad/schema_salad/add_dictlist.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/add_dictlist.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/add_dictlist.py\n@@ -1,8 +1,7 @@\n import sys\n-if sys.version_info >= (2,7):\n- import typing\n+from typing import Any, Dict\n \n-def add_dictlist(di, key, val):\n+def add_dictlist(di, key, val): # type: (Dict, Any, Any) -> None\n if key not in di:\n di[key] = []\n di[key].append(val)\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/aslist.py b/cwltool/schemas/draft-4/salad/schema_salad/aslist.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/aslist.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/aslist.py\n@@ -1,8 +1,7 @@\n import sys\n-if sys.version_info >= (2,7):\n- import typing\n+from typing import Any, List\n \n-def aslist(l):\n+def aslist(l): # type: (Any) -> List\n \"\"\"Convenience function to wrap single items and lists, and return lists unchanged.\"\"\"\n \n if isinstance(l, list):\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/flatten.py b/cwltool/schemas/draft-4/salad/schema_salad/flatten.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/flatten.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/flatten.py\n@@ -1,9 +1,9 @@\n import sys\n-if sys.version_info >= (2,7):\n- import typing\n+from typing import Any, Tuple\n \n # http://rightfootin.blogspot.com/2006/09/more-on-python-flatten.html\n def flatten(l, ltypes=(list, tuple)):\n+ # type: (Any, Any) -> Any\n if l is None:\n return []\n if not isinstance(l, ltypes):\n@@ -21,4 +21,4 @@ def flatten(l, ltypes=(list, tuple)):\n else:\n l[i:i + 1] = l[i]\n i += 1\n- return ltype(l)\n+ return ltype(l) # type: ignore\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/jsonld_context.py b/cwltool/schemas/draft-4/salad/schema_salad/jsonld_context.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/jsonld_context.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/jsonld_context.py\n@@ -1,6 +1,11 @@\n+import collections\n import shutil\n import json\n-import yaml\n+import ruamel.yaml as yaml\n+try:\n+ from ruamel.yaml import CSafeLoader as SafeLoader\n+except ImportError:\n+ from ruamel.yaml import SafeLoader # type: ignore\n import os\n import subprocess\n import copy\n@@ -11,62 +16,74 @@\n from rdflib import Graph, URIRef\n import rdflib.namespace\n from rdflib.namespace import RDF, RDFS\n-try:\n- import urlparse\n-except ImportError:\n- import urllib.parse as urlparse\n- unicode=str\n- basestring=str\n+import urlparse\n import logging\n from .aslist import aslist\n-if sys.version_info >= (2,7):\n- import typing\n+from typing import Any, cast, Dict, Iterable, Tuple, Union\n+from .ref_resolver import Loader\n \n _logger = logging.getLogger(\"salad\")\n \n+\n def pred(datatype, field, name, context, defaultBase, namespaces):\n+ # type: (Dict[str, Union[Dict, str]], Dict, str, Loader.ContextType, str, Dict[str, rdflib.namespace.Namespace]) -> Union[Dict, str]\n split = urlparse.urlsplit(name)\n \n- v = None\n+ vee = None # type: Union[str, unicode]\n \n if split.scheme:\n- v = name\n- (ns, ln) = rdflib.namespace.split_uri(unicode(v))\n+ vee = name\n+ (ns, ln) = rdflib.namespace.split_uri(unicode(vee))\n name = ln\n if ns[0:-1] in namespaces:\n- v = unicode(namespaces[ns[0:-1]][ln])\n- _logger.debug(\"name, v %s %s\", name, v)\n+ vee = unicode(namespaces[ns[0:-1]][ln])\n+ _logger.debug(\"name, v %s %s\", name, vee)\n+\n+ v = None # type: Any\n \n if field and \"jsonldPredicate\" in field:\n if isinstance(field[\"jsonldPredicate\"], dict):\n v = {}\n for k, val in field[\"jsonldPredicate\"].items():\n- v[(\"@\"+k[1:] if k.startswith(\"_\") else k)] = val\n+ v[(\"@\" + k[1:] if k.startswith(\"_\") else k)] = val\n else:\n v = field[\"jsonldPredicate\"]\n elif \"jsonldPredicate\" in datatype:\n- for d in datatype[\"jsonldPredicate\"]:\n- if d[\"symbol\"] == name:\n- v = d[\"predicate\"]\n+ if isinstance(datatype[\"jsonldPredicate\"], collections.Iterable):\n+ for d in datatype[\"jsonldPredicate\"]:\n+ if isinstance(d, dict):\n+ if d[\"symbol\"] == name:\n+ v = d[\"predicate\"]\n+ else:\n+ raise Exception(\n+ \"entries in the jsonldPredicate List must be \"\n+ \"Dictionaries\")\n+ else:\n+ raise Exception(\"jsonldPredicate must be a List of Dictionaries.\")\n # if not v:\n # if field and \"jsonldPrefix\" in field:\n # defaultBase = field[\"jsonldPrefix\"]\n # elif \"jsonldPrefix\" in datatype:\n # defaultBase = datatype[\"jsonldPrefix\"]\n \n- if not v:\n- v = defaultBase + name\n+ ret = v or vee\n+\n+ if not ret:\n+ ret = defaultBase + name\n \n if name in context:\n- if context[name] != v:\n- raise Exception(\"Predicate collision on %s, '%s' != '%s'\" % (name, context[name], v))\n+ if context[name] != ret:\n+ raise Exception(\"Predicate collision on %s, '%s' != '%s'\" %\n+ (name, context[name], ret))\n else:\n- _logger.debug(\"Adding to context '%s' %s (%s)\", name, v, type(v))\n- context[name] = v\n+ _logger.debug(\"Adding to context '%s' %s (%s)\", name, ret, type(ret))\n+ context[name] = ret\n+\n+ return ret\n \n- return v\n \n def process_type(t, g, context, defaultBase, namespaces, defaultPrefix):\n+ # type: (Dict[str, Any], Graph, Loader.ContextType, str, Dict[str, rdflib.namespace.Namespace], str) -> None\n if t[\"type\"] == \"record\":\n recordname = t[\"name\"]\n \n@@ -86,12 +103,14 @@ def process_type(t, g, context, defaultBase, namespaces, defaultPrefix):\n predicate = \"%s:%s\" % (defaultPrefix, recordname)\n \n if context.get(recordname, predicate) != predicate:\n- raise Exception(\"Predicate collision on '%s', '%s' != '%s'\" % (recordname, context[recordname], predicate))\n+ raise Exception(\"Predicate collision on '%s', '%s' != '%s'\" % (\n+ recordname, context[recordname], predicate))\n \n if not recordname:\n raise Exception()\n \n- _logger.debug(\"Adding to context '%s' %s (%s)\", recordname, predicate, type(predicate))\n+ _logger.debug(\"Adding to context '%s' %s (%s)\",\n+ recordname, predicate, type(predicate))\n context[recordname] = predicate\n \n for i in t.get(\"fields\", []):\n@@ -119,7 +138,8 @@ def process_type(t, g, context, defaultBase, namespaces, defaultPrefix):\n # TODO generate range from datatype.\n \n if isinstance(i[\"type\"], dict) and \"name\" in i[\"type\"]:\n- process_type(i[\"type\"], g, context, defaultBase, namespaces, defaultPrefix)\n+ process_type(i[\"type\"], g, context, defaultBase,\n+ namespaces, defaultPrefix)\n \n if \"extends\" in t:\n for e in aslist(t[\"extends\"]):\n@@ -132,31 +152,26 @@ def process_type(t, g, context, defaultBase, namespaces, defaultPrefix):\n \n \n def salad_to_jsonld_context(j, schema_ctx):\n- context = {}\n+ # type: (Iterable, Dict[str, Any]) -> Tuple[Loader.ContextType, Graph]\n+ context = {} # type: Loader.ContextType\n namespaces = {}\n g = Graph()\n defaultPrefix = \"\"\n \n- for k,v in schema_ctx.items():\n+ for k, v in schema_ctx.items():\n context[k] = v\n namespaces[k] = rdflib.namespace.Namespace(v)\n \n if \"@base\" in context:\n- defaultBase = context[\"@base\"]\n+ defaultBase = cast(str, context[\"@base\"])\n del context[\"@base\"]\n else:\n defaultBase = \"\"\n \n- for k,v in namespaces.items():\n+ for k, v in namespaces.items():\n g.bind(k, v)\n \n for t in j:\n process_type(t, g, context, defaultBase, namespaces, defaultPrefix)\n \n return (context, g)\n-\n-if __name__ == \"__main__\":\n- with open(sys.argv[1]) as f:\n- j = yaml.load(f)\n- (ctx, g) = salad_to_jsonld_context(j)\n- print(json.dumps(ctx, indent=4, sort_keys=True))\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/main.py b/cwltool/schemas/draft-4/salad/schema_salad/main.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/main.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/main.py\n@@ -9,31 +9,29 @@\n import json\n from rdflib import Graph, plugin\n from rdflib.serializer import Serializer\n-import yaml\n import os\n-try:\n- import urlparse\n-except ImportError:\n- import urllib.parse as urlparse\n+import urlparse\n \n from .ref_resolver import Loader\n from . import validate\n-if sys.version_info >= (2,7):\n- import typing\n+from typing import Any, Dict, List, Union\n \n _logger = logging.getLogger(\"salad\")\n \n from rdflib.plugin import register, Parser\n-import rdflib_jsonld.parser\n register('json-ld', Parser, 'rdflib_jsonld.parser', 'JsonLDParser')\n \n+\n def printrdf(workflow, wf, ctx, sr):\n- g = Graph().parse(data=json.dumps(wf), format='json-ld', location=workflow, context=ctx)\n+ # type: (str, Union[List, Dict[Any, Any], str, unicode], Dict[unicode, Any], str) -> None\n+ g = Graph().parse(data=json.dumps(wf), format='json-ld',\n+ location=workflow, context=ctx)\n print(g.serialize(format=sr))\n \n-def main(args=None):\n- if args is None:\n- args = sys.argv[1:]\n+\n+def main(argsl=None): # type: (List[str]) -> int\n+ if argsl is None:\n+ argsl = sys.argv[1:]\n \n parser = argparse.ArgumentParser()\n parser.add_argument(\"--rdf-serializer\",\n@@ -41,15 +39,23 @@ def main(args=None):\n default=\"turtle\")\n \n exgroup = parser.add_mutually_exclusive_group()\n- exgroup.add_argument(\"--print-jsonld-context\", action=\"store_true\", help=\"Print JSON-LD context for schema\")\n- exgroup.add_argument(\"--print-rdfs\", action=\"store_true\", help=\"Print RDF schema\")\n- exgroup.add_argument(\"--print-avro\", action=\"store_true\", help=\"Print Avro schema\")\n-\n- exgroup.add_argument(\"--print-rdf\", action=\"store_true\", help=\"Print corresponding RDF graph for document\")\n- exgroup.add_argument(\"--print-pre\", action=\"store_true\", help=\"Print document after preprocessing\")\n- exgroup.add_argument(\"--print-index\", action=\"store_true\", help=\"Print node index\")\n- exgroup.add_argument(\"--print-metadata\", action=\"store_true\", help=\"Print document metadata\")\n- exgroup.add_argument(\"--version\", action=\"store_true\", help=\"Print version\")\n+ exgroup.add_argument(\"--print-jsonld-context\", action=\"store_true\",\n+ help=\"Print JSON-LD context for schema\")\n+ exgroup.add_argument(\n+ \"--print-rdfs\", action=\"store_true\", help=\"Print RDF schema\")\n+ exgroup.add_argument(\"--print-avro\", action=\"store_true\",\n+ help=\"Print Avro schema\")\n+\n+ exgroup.add_argument(\"--print-rdf\", action=\"store_true\",\n+ help=\"Print corresponding RDF graph for document\")\n+ exgroup.add_argument(\"--print-pre\", action=\"store_true\",\n+ help=\"Print document after preprocessing\")\n+ exgroup.add_argument(\n+ \"--print-index\", action=\"store_true\", help=\"Print node index\")\n+ exgroup.add_argument(\"--print-metadata\",\n+ action=\"store_true\", help=\"Print document metadata\")\n+ exgroup.add_argument(\"--version\", action=\"store_true\",\n+ help=\"Print version\")\n \n exgroup = parser.add_mutually_exclusive_group()\n exgroup.add_argument(\"--strict\", action=\"store_true\", help=\"Strict validation (unrecognized or out of place fields are error)\",\n@@ -58,14 +64,17 @@ def main(args=None):\n default=True, dest=\"strict\")\n \n exgroup = parser.add_mutually_exclusive_group()\n- exgroup.add_argument(\"--verbose\", action=\"store_true\", help=\"Default logging\")\n- exgroup.add_argument(\"--quiet\", action=\"store_true\", help=\"Only print warnings and errors.\")\n- exgroup.add_argument(\"--debug\", action=\"store_true\", help=\"Print even more logging\")\n+ exgroup.add_argument(\"--verbose\", action=\"store_true\",\n+ help=\"Default logging\")\n+ exgroup.add_argument(\"--quiet\", action=\"store_true\",\n+ help=\"Only print warnings and errors.\")\n+ exgroup.add_argument(\"--debug\", action=\"store_true\",\n+ help=\"Print even more logging\")\n \n parser.add_argument(\"schema\", type=str)\n parser.add_argument(\"document\", type=str, nargs=\"?\", default=None)\n \n- args = parser.parse_args(args)\n+ args = parser.parse_args(argsl)\n \n if args.quiet:\n _logger.setLevel(logging.WARN)\n@@ -89,7 +98,16 @@ def main(args=None):\n if not urlparse.urlparse(schema_uri)[0]:\n schema_uri = \"file://\" + os.path.abspath(schema_uri)\n schema_raw_doc = metaschema_loader.fetch(schema_uri)\n- schema_doc, schema_metadata = metaschema_loader.resolve_all(schema_raw_doc, schema_uri)\n+\n+ try:\n+ schema_doc, schema_metadata = metaschema_loader.resolve_all(\n+ schema_raw_doc, schema_uri)\n+ except (validate.ValidationException) as e:\n+ _logger.error(\"Schema `%s` failed link checking:\\n%s\",\n+ args.schema, e, exc_info=(e if args.debug else False))\n+ _logger.debug(\"Index is %s\", metaschema_loader.idx.keys())\n+ _logger.debug(\"Vocabulary is %s\", metaschema_loader.vocab.keys())\n+ return 1\n \n # Optionally print the schema after ref resolution\n if not args.document and args.print_pre:\n@@ -100,20 +118,13 @@ def main(args=None):\n print(json.dumps(metaschema_loader.idx.keys(), indent=4))\n return 0\n \n- # Validate links in the schema document\n- try:\n- metaschema_loader.validate_links(schema_doc)\n- except (validate.ValidationException) as e:\n- _logger.error(\"Schema `%s` failed link checking:\\n%s\", args.schema, e, exc_info=(e if args.debug else False))\n- _logger.debug(\"Index is %s\", metaschema_loader.idx.keys())\n- _logger.debug(\"Vocabulary is %s\", metaschema_loader.vocab.keys())\n- return 1\n-\n # Validate the schema document against the metaschema\n try:\n- schema.validate_doc(metaschema_names, schema_doc, metaschema_loader, args.strict)\n+ schema.validate_doc(metaschema_names, schema_doc,\n+ metaschema_loader, args.strict)\n except validate.ValidationException as e:\n- _logger.error(\"While validating schema `%s`:\\n%s\" % (args.schema, str(e)))\n+ _logger.error(\"While validating schema `%s`:\\n%s\" %\n+ (args.schema, str(e)))\n return 1\n \n # Get the json-ld context and RDFS representation from the schema\n@@ -127,11 +138,18 @@ def main(args=None):\n # Create the loader that will be used to load the target document.\n document_loader = Loader(schema_ctx)\n \n- # Make the Avro validation that will be used to validate the target document\n- (avsc_names, avsc_obj) = schema.make_avro_schema(schema_doc, document_loader)\n+ # Make the Avro validation that will be used to validate the target\n+ # document\n+ if isinstance(schema_doc, list):\n+ (avsc_names, avsc_obj) = schema.make_avro_schema(\n+ schema_doc, document_loader)\n+ else:\n+ _logger.error(\"Schema `%s` must be a list.\", args.schema)\n+ return 1\n \n if isinstance(avsc_names, Exception):\n- _logger.error(\"Schema `%s` error:\\n%s\", args.schema, avsc_names, exc_info=(avsc_names if args.debug else False))\n+ _logger.error(\"Schema `%s` error:\\n%s\", args.schema,\n+ avsc_names, exc_info=(avsc_names if args.debug else False))\n if args.print_avro:\n print(json.dumps(avsc_obj, indent=4))\n return 1\n@@ -168,7 +186,8 @@ def main(args=None):\n doc = \"file://\" + os.path.abspath(uri)\n document, doc_metadata = document_loader.resolve_ref(uri)\n except (validate.ValidationException, RuntimeError) as e:\n- _logger.error(\"Document `%s` failed validation:\\n%s\", args.document, e, exc_info=(e if args.debug else False))\n+ _logger.error(\"Document `%s` failed validation:\\n%s\",\n+ args.document, e, exc_info=(e if args.debug else False))\n return 1\n \n # Optionally print the document after ref resolution\n@@ -180,19 +199,13 @@ def main(args=None):\n print(json.dumps(document_loader.idx.keys(), indent=4))\n return 0\n \n- # Validate links in the target document\n- try:\n- document_loader.validate_links(document)\n- except (validate.ValidationException) as e:\n- _logger.error(\"Document `%s` failed link checking:\\n%s\", args.document, e, exc_info=(e if args.debug else False))\n- _logger.debug(\"Index is %s\", json.dumps(document_loader.idx.keys(), indent=4))\n- return 1\n-\n # Validate the schema document against the metaschema\n try:\n- schema.validate_doc(avsc_names, document, document_loader, args.strict)\n+ schema.validate_doc(avsc_names, document,\n+ document_loader, args.strict)\n except validate.ValidationException as e:\n- _logger.error(\"While validating document `%s`:\\n%s\" % (args.document, str(e)))\n+ _logger.error(\"While validating document `%s`:\\n%s\" %\n+ (args.document, str(e)))\n return 1\n \n # Optionally convert the document to RDF\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/makedoc.py b/cwltool/schemas/draft-4/salad/schema_salad/makedoc.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/makedoc.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/makedoc.py\n@@ -1,30 +1,23 @@\n import mistune\n from . import schema\n import json\n-import yaml\n import os\n import copy\n import re\n import sys\n-try:\n- import StringIO\n-except ImportError:\n- from io import StringIO\n+import StringIO\n import logging\n-try:\n- import urlparse\n-except ImportError:\n- import urllib.parse as urlparse\n+import urlparse\n from .aslist import aslist\n from .add_dictlist import add_dictlist\n import re\n import argparse\n-if sys.version_info >= (2,7):\n- import typing\n+from typing import Any, IO, Union\n \n _logger = logging.getLogger(\"salad\")\n \n-def has_types(items):\n+\n+def has_types(items): # type: (Any) -> List[basestring]\n r = [] # type: List\n if isinstance(items, dict):\n if items[\"type\"] == \"https://w3id.org/cwl/salad#record\":\n@@ -41,36 +34,46 @@ def has_types(items):\n return [items]\n return []\n \n+\n def linkto(item):\n _, frg = urlparse.urldefrag(item)\n return \"[%s](#%s)\" % (frg, to_id(frg))\n \n+\n class MyRenderer(mistune.Renderer):\n+\n+ def __init__(self): # type: () -> None\n+ super(mistune.Renderer, self).__init__()\n+ self.options = {}\n+\n def header(self, text, level, raw=None):\n return \"\"\"%s\"\"\" % (level, to_id(text), text, level)\n \n-def to_id(text):\n+\n+def to_id(text): # type: (Union[str, unicode]) -> Union[str, unicode]\n textid = text\n if text[0] in (\"0\", \"1\", \"2\", \"3\", \"4\", \"5\", \"6\", \"7\", \"8\", \"9\"):\n try:\n- textid = text[text.index(\" \")+1:]\n+ textid = text[text.index(\" \") + 1:]\n except ValueError:\n pass\n textid = textid.replace(\" \", \"_\")\n return textid\n \n+\n class ToC(object):\n- def __init__(self):\n+\n+ def __init__(self): # type: () -> None\n self.first_toc_entry = True\n self.numbering = [0]\n self.toc = \"\"\n self.start_numbering = True\n \n- def add_entry(self, thisdepth, title):\n+ def add_entry(self, thisdepth, title): # type: (int, str) -> str\n depth = len(self.numbering)\n if thisdepth < depth:\n self.toc += \"\"\n- for n in range(0, depth-thisdepth):\n+ for n in range(0, depth - thisdepth):\n self.numbering.pop()\n self.toc += \"\"\n self.numbering[-1] += 1\n@@ -84,16 +87,17 @@ def add_entry(self, thisdepth, title):\n self.numbering.append(1)\n \n if self.start_numbering:\n- num = \"%i.%s\" % (self.numbering[0], \".\".join([str(n) for n in self.numbering[1:]]))\n+ num = \"%i.%s\" % (self.numbering[0], \".\".join(\n+ [str(n) for n in self.numbering[1:]]))\n else:\n num = \"\"\n- self.toc += \"\"\"
  • %s %s
      \\n\"\"\" %(to_id(title),\n- num, title)\n+ self.toc += \"\"\"
    1. %s %s
        \\n\"\"\" % (to_id(title),\n+ num, title)\n return num\n \n- def contents(self, id):\n+ def contents(self, idn): # type: (str) -> str\n c = \"\"\"

        Table of contents

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