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{"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 \"\"\"<h%i id=\"%s\">%s</h%i>\"\"\" % (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 += \"</ol>\"\n- for n in range(0, depth-thisdepth):\n+ for n in range(0, depth - thisdepth):\n self.numbering.pop()\n self.toc += \"</li></ol>\"\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 += \"\"\"<li><a href=\"#%s\">%s %s</a><ol>\\n\"\"\" %(to_id(title),\n- num, title)\n+ self.toc += \"\"\"<li><a href=\"#%s\">%s %s</a><ol>\\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 = \"\"\"<h1 id=\"%s\">Table of contents</h1>\n- <nav class=\"tocnav\"><ol>%s\"\"\" % (id, self.toc)\n+ <nav class=\"tocnav\"><ol>%s\"\"\" % (idn, self.toc)\n c += \"</ol>\"\n for i in range(0, len(self.numbering)):\n c += \"</li></ol>\"\n@@ -111,7 +115,8 @@ def contents(self, id):\n \"https://w3id.org/cwl/salad#enum\",\n \"https://w3id.org/cwl/salad#array\")\n \n-def number_headings(toc, maindoc):\n+\n+def number_headings(toc, maindoc): # type: (ToC, str) -> str\n mdlines = []\n skip = False\n for line in maindoc.splitlines():\n@@ -133,19 +138,27 @@ def number_headings(toc, maindoc):\n maindoc = '\\n'.join(mdlines)\n return maindoc\n \n-def fix_doc(doc):\n+\n+def fix_doc(doc): # type: (Union[List[str], str]) -> str\n if isinstance(doc, list):\n- doc = \"\".join(doc)\n- return \"\\n\".join([re.sub(r\"<([^>@]+@[^>]+)>\", r\"[\\1](mailto:\\1)\", d) for d in doc.splitlines()])\n+ docstr = \"\".join(doc)\n+ else:\n+ docstr = doc\n+ return \"\\n\".join(\n+ [re.sub(r\"<([^>@]+@[^>]+)>\", r\"[\\1](mailto:\\1)\", d)\n+ for d in docstr.splitlines()])\n+\n \n class RenderType(object):\n+\n def __init__(self, toc, j, renderlist, redirects):\n+ # type: (ToC, List[Dict], str, Dict) -> None\n self.typedoc = StringIO.StringIO()\n self.toc = toc\n- self.subs = {} # type: Dict\n- self.docParent = {} # type: Dict\n- self.docAfter = {} # type: Dict\n- self.rendered = set() # type: Set\n+ self.subs = {} # type: Dict[str, str]\n+ self.docParent = {} # type: Dict[str, List]\n+ self.docAfter = {} # type: Dict[str, List]\n+ self.rendered = set() # type: Set[str]\n self.redirects = redirects\n self.title = None # type: str\n \n@@ -153,7 +166,7 @@ def __init__(self, toc, j, renderlist, redirects):\n if \"extends\" in t:\n for e in aslist(t[\"extends\"]):\n add_dictlist(self.subs, e, t[\"name\"])\n- #if \"docParent\" not in t and \"docAfter\" not in t:\n+ # if \"docParent\" not in t and \"docAfter\" not in t:\n # add_dictlist(self.docParent, e, t[\"name\"])\n \n if t.get(\"docParent\"):\n@@ -166,7 +179,7 @@ def __init__(self, toc, j, renderlist, redirects):\n if t.get(\"docAfter\"):\n add_dictlist(self.docAfter, t[\"docAfter\"], t[\"name\"])\n \n- _, _, metaschema_loader = schema.get_metaschema()\n+ metaschema_loader = schema.get_metaschema()[2]\n alltypes = schema.extend_and_specialize(j, metaschema_loader)\n \n self.typemap = {} # type: Dict\n@@ -187,7 +200,7 @@ def __init__(self, toc, j, renderlist, redirects):\n _, frg2 = urlparse.urldefrag(f[\"name\"])\n self.uses[tp].append((frg1, frg2))\n if tp not in basicTypes and tp not in self.record_refs[t[\"name\"]]:\n- self.record_refs[t[\"name\"]].append(tp)\n+ self.record_refs[t[\"name\"]].append(tp)\n except KeyError as e:\n _logger.error(\"Did not find 'type' in %s\", t)\n raise\n@@ -201,6 +214,7 @@ def __init__(self, toc, j, renderlist, redirects):\n self.render_type(f, 1)\n \n def typefmt(self, tp, redirects, nbsp=False):\n+ # type: (Any, Dict[str, str], bool) -> Union[str, unicode]\n global primitiveType\n if isinstance(tp, list):\n if nbsp and len(tp) <= 3:\n@@ -231,8 +245,7 @@ def typefmt(self, tp, redirects, nbsp=False):\n tp = frg\n return \"\"\"<a href=\"#%s\">%s</a>\"\"\" % (to_id(tp), tp)\n \n-\n- def render_type(self, f, depth):\n+ def render_type(self, f, depth): # type: (Dict[str, Any], int) -> None\n if f[\"name\"] in self.rendered or f[\"name\"] in self.redirects:\n return\n self.rendered.add(f[\"name\"])\n@@ -248,6 +261,7 @@ def render_type(self, f, depth):\n f[\"doc\"] = \"\"\n \n def extendsfrom(item, ex):\n+ # type: (Dict[str, Any], List[Dict[str, Any]]) -> None\n if \"extends\" in item:\n for e in aslist(item[\"extends\"]):\n ex.insert(0, self.typemap[e])\n@@ -262,8 +276,9 @@ def extendsfrom(item, ex):\n for i in e[\"doc\"]:\n idx = i.find(\":\")\n if idx > -1:\n- enumDesc[i[:idx]] = i[idx+1:]\n- e[\"doc\"] = [i for i in e[\"doc\"] if i.find(\":\") == -1 or i.find(\" \") < i.find(\":\")]\n+ enumDesc[i[:idx]] = i[idx + 1:]\n+ e[\"doc\"] = [i for i in e[\"doc\"] if i.find(\n+ \":\") == -1 or i.find(\" \") < i.find(\":\")]\n \n f[\"doc\"] = fix_doc(f[\"doc\"])\n \n@@ -294,15 +309,16 @@ def extendsfrom(item, ex):\n if f[\"type\"] == \"documentation\":\n f[\"doc\"] = number_headings(self.toc, f[\"doc\"])\n \n- #if \"extends\" in f:\n+ # if \"extends\" in f:\n # doc += \"\\n\\nExtends \"\n # doc += \", \".join([\" %s\" % linkto(ex) for ex in aslist(f[\"extends\"])])\n- #if f[\"name\"] in self.subs:\n+ # if f[\"name\"] in self.subs:\n # doc += \"\\n\\nExtended by\"\n # doc += \", \".join([\" %s\" % linkto(s) for s in self.subs[f[\"name\"]]])\n- #if f[\"name\"] in self.uses:\n+ # if f[\"name\"] in self.uses:\n # doc += \"\\n\\nReferenced by\"\n- # doc += \", \".join([\" [%s.%s](#%s)\" % (s[0], s[1], to_id(s[0])) for s in self.uses[f[\"name\"]]])\n+ # doc += \", \".join([\" [%s.%s](#%s)\" % (s[0], s[1], to_id(s[0]))\n+ # for s in self.uses[f[\"name\"]]])\n \n doc = doc + \"\\n\\n\" + f[\"doc\"]\n \n@@ -323,16 +339,19 @@ def extendsfrom(item, ex):\n opt = True\n \n desc = i[\"doc\"]\n- #if \"inherited_from\" in i:\n+ # if \"inherited_from\" in i:\n # desc = \"%s _Inherited from %s_\" % (desc, linkto(i[\"inherited_from\"]))\n \n- frg = schema.avro_name(i[\"name\"])\n- tr = \"<td><code>%s</code></td><td>%s</td><td>%s</td><td>%s</td>\" % (frg, self.typefmt(tp, self.redirects), opt, mistune.markdown(desc))\n+ rfrg = schema.avro_name(i[\"name\"])\n+ tr = \"<td><code>%s</code></td><td>%s</td><td>%s</td>\"\\\n+ \"<td>%s</td>\" % (\n+ rfrg, self.typefmt(tp, self.redirects), opt,\n+ mistune.markdown(desc))\n if opt:\n required.append(tr)\n else:\n optional.append(tr)\n- for i in required+optional:\n+ for i in required + optional:\n doc += \"<tr>\" + i + \"</tr>\"\n doc += \"\"\"</table>\"\"\"\n elif f[\"type\"] == \"enum\":\n@@ -342,30 +361,34 @@ def extendsfrom(item, ex):\n for e in ex:\n for i in e.get(\"symbols\", []):\n doc += \"<tr>\"\n- frg = schema.avro_name(i)\n- doc += \"<td><code>%s</code></td><td>%s</td>\" % (frg, enumDesc.get(frg, \"\"))\n+ efrg = schema.avro_name(i)\n+ doc += \"<td><code>%s</code></td><td>%s</td>\" % (\n+ efrg, enumDesc.get(efrg, \"\"))\n doc += \"</tr>\"\n doc += \"\"\"</table>\"\"\"\n f[\"doc\"] = doc\n \n self.typedoc.write(f[\"doc\"])\n \n- subs = self.docParent.get(f[\"name\"], []) + self.record_refs.get(f[\"name\"], [])\n+ subs = self.docParent.get(f[\"name\"], []) + \\\n+ self.record_refs.get(f[\"name\"], [])\n if len(subs) == 1:\n self.render_type(self.typemap[subs[0]], depth)\n else:\n for s in subs:\n- self.render_type(self.typemap[s], depth+1)\n+ self.render_type(self.typemap[s], depth + 1)\n \n for s in self.docAfter.get(f[\"name\"], []):\n self.render_type(self.typemap[s], depth)\n \n+\n def avrold_doc(j, outdoc, renderlist, redirects, brand, brandlink):\n+ # type: (List[Dict[unicode, Any]], IO[Any], str, Dict, str, str) -> None\n toc = ToC()\n toc.start_numbering = False\n \n rt = RenderType(toc, j, renderlist, redirects)\n- content = rt.typedoc.getvalue()\n+ content = rt.typedoc.getvalue() # type: unicode\n \n outdoc.write(\"\"\"\n <!DOCTYPE html>\n@@ -452,22 +475,24 @@ def avrold_doc(j, outdoc, renderlist, redirects, brand, brandlink):\n \n args = parser.parse_args()\n \n- s = []\n+ s = [] # type: List[Dict[unicode, Any]]\n a = args.schema\n with open(a) as f:\n if a.endswith(\"md\"):\n s.append({\"name\": os.path.splitext(os.path.basename(a))[0],\n- \"type\": \"documentation\",\n- \"doc\": f.read().decode(\"utf-8\")\n- })\n+ \"type\": \"documentation\",\n+ \"doc\": f.read().decode(\"utf-8\")\n+ })\n else:\n uri = \"file://\" + os.path.abspath(a)\n- _, _, metaschema_loader = schema.get_metaschema()\n+ metaschema_loader = schema.get_metaschema()[2]\n j, schema_metadata = metaschema_loader.resolve_ref(uri, \"\")\n if isinstance(j, list):\n s.extend(j)\n- else:\n+ elif isinstance(j, dict):\n s.append(j)\n+ else:\n+ raise ValueError(\"Schema must resolve to a list or a dict\")\n \n primitiveType = args.primtype\n redirect = {}\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/ref_resolver.py b/cwltool/schemas/draft-4/salad/schema_salad/ref_resolver.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/ref_resolver.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/ref_resolver.py\n@@ -5,31 +5,30 @@\n import logging\n import collections\n import requests\n+import urlparse\n+import re\n+import ruamel.yaml as yaml\n try:\n- import urlparse\n-except:\n- import urllib.parse as urlparse\n-import yaml\n+ from ruamel.yaml import CSafeLoader as SafeLoader\n+except ImportError:\n+ from ruamel.yaml import SafeLoader # type: ignore\n from . import validate\n import pprint\n-try:\n- from StringIO import StringIO\n-except ImportError:\n- from io import StringIO\n- unicode=str\n- basestring=str\n+from StringIO import StringIO\n from .aslist import aslist\n+from .flatten import flatten\n import rdflib\n from rdflib.namespace import RDF, RDFS, OWL\n+from rdflib.plugins.parsers.notation3 import BadSyntax\n import xml.sax\n-if sys.version_info >= (2,7):\n- import typing\n- from typing import Union, Tuple\n+from typing import (Any, AnyStr, Callable, cast, Dict, List, Iterable, Tuple,\n+ TypeVar, Union)\n \n _logger = logging.getLogger(\"salad\")\n \n class NormDict(dict):\n- def __init__(self, normalize=unicode):\n+\n+ def __init__(self, normalize=unicode): # type: (type) -> None\n super(NormDict, self).__init__()\n self.normalize = normalize\n \n@@ -45,6 +44,7 @@ def __delitem__(self, key):\n def __contains__(self, key):\n return super(NormDict, self).__contains__(self.normalize(key))\n \n+\n def merge_properties(a, b):\n c = {}\n for i in a:\n@@ -59,22 +59,32 @@ def merge_properties(a, b):\n \n return c\n \n-def SubLoader(loader):\n- return Loader(loader.ctx, schemagraph=loader.graph, foreign_properties=loader.foreign_properties, idx=loader.idx, cache=loader.cache)\n+\n+def SubLoader(loader): # type: (Loader) -> Loader\n+ return Loader(loader.ctx, schemagraph=loader.graph,\n+ foreign_properties=loader.foreign_properties, idx=loader.idx,\n+ cache=loader.cache)\n+\n \n class Loader(object):\n- def __init__(self, ctx, schemagraph=None, foreign_properties=None, idx=None, cache=None):\n+\n+ ContextType = Dict[unicode, Union[Dict, unicode, Iterable[unicode]]]\n+ DocumentType = TypeVar('DocumentType', List, Dict[unicode, Any])\n+\n+ def __init__(self, ctx, schemagraph=None, foreign_properties=None,\n+ idx=None, cache=None):\n+ # type: (Loader.ContextType, rdflib.Graph, Set[unicode], Dict[unicode, Union[List, Dict[unicode, Any], unicode]], Dict[unicode, Any]) -> None\n normalize = lambda url: urlparse.urlsplit(url).geturl()\n if idx is not None:\n self.idx = idx\n else:\n self.idx = NormDict(normalize)\n \n- self.ctx = {} # type: Dict[str, Union[str, dict, basestring]]\n+ self.ctx = {} # type: Loader.ContextType\n if schemagraph is not None:\n self.graph = schemagraph\n else:\n- self.graph = rdflib.Graph()\n+ self.graph = rdflib.graph.Graph()\n \n if foreign_properties is not None:\n self.foreign_properties = foreign_properties\n@@ -86,41 +96,49 @@ def __init__(self, ctx, schemagraph=None, foreign_properties=None, idx=None, cac\n else:\n self.cache = {}\n \n- self.url_fields = set() # type: Set[str]\n- self.vocab_fields = set() # type: Set\n- self.identifiers = set() # type: Set\n- self.identity_links = set() # type: Set\n- self.standalone = set() # type: Set\n- self.nolinkcheck = set() # type: Set\n- self.vocab = {} # type: Dict\n- self.rvocab = {} # type: Dict\n+ self.url_fields = None # type: Set[unicode]\n+ self.scoped_ref_fields = None # type: Dict[unicode, int]\n+ self.vocab_fields = None # type: Set[unicode]\n+ self.identifiers = None # type: Set[unicode]\n+ self.identity_links = None # type: Set[unicode]\n+ self.standalone = None # type: Set[unicode]\n+ self.nolinkcheck = None # type: Set[unicode]\n+ self.vocab = {} # type: Dict[unicode, unicode]\n+ self.rvocab = {} # type: Dict[unicode, unicode]\n+ self.idmap = None # type: Dict[unicode, Any]\n+ self.mapPredicate = None # type: Dict[unicode, unicode]\n+ self.type_dsl_fields = None # type: Set[unicode]\n \n self.add_context(ctx)\n \n- def expand_url(self, url, base_url, scoped=False, vocab_term=False):\n- if url in (\"@id\", \"@type\"):\n+ def expand_url(self, url, base_url, scoped_id=False, vocab_term=False, scoped_ref=None):\n+ # type: (unicode, unicode, bool, bool, int) -> unicode\n+ if url in (u\"@id\", u\"@type\"):\n return url\n \n if vocab_term and url in self.vocab:\n return url\n \n- if self.vocab and \":\" in url:\n- prefix = url.split(\":\")[0]\n+ if self.vocab and u\":\" in url:\n+ prefix = url.split(u\":\")[0]\n if prefix in self.vocab:\n- url = self.vocab[prefix] + url[len(prefix)+1:]\n+ url = self.vocab[prefix] + url[len(prefix) + 1:]\n \n split = urlparse.urlsplit(url)\n \n- if split.scheme or url.startswith(\"$(\") or url.startswith(\"${\"):\n+ if split.scheme or url.startswith(u\"$(\") or url.startswith(u\"${\"):\n pass\n- elif scoped and not split.fragment:\n+ elif scoped_id and not split.fragment:\n splitbase = urlparse.urlsplit(base_url)\n- frg = \"\"\n+ frg = u\"\"\n if splitbase.fragment:\n- frg = splitbase.fragment + \"/\" + split.path\n+ frg = splitbase.fragment + u\"/\" + split.path\n else:\n frg = split.path\n- url = urlparse.urlunsplit((splitbase.scheme, splitbase.netloc, splitbase.path, splitbase.query, frg))\n+ url = urlparse.urlunsplit(\n+ (splitbase.scheme, splitbase.netloc, splitbase.path, splitbase.query, frg))\n+ elif scoped_ref is not None and not split.fragment:\n+ pass\n else:\n url = urlparse.urljoin(base_url, url)\n \n@@ -129,43 +147,56 @@ def expand_url(self, url, base_url, scoped=False, vocab_term=False):\n else:\n return url\n \n- def _add_properties(self, s):\n- for _, _, rng in self.graph.triples( (s, RDFS.range, None) ):\n- literal = ((str(rng).startswith(\"http://www.w3.org/2001/XMLSchema#\") and not str(rng) == \"http://www.w3.org/2001/XMLSchema#anyURI\") or\n- str(rng) == \"http://www.w3.org/2000/01/rdf-schema#Literal\")\n+ def _add_properties(self, s): # type: (unicode) -> None\n+ for _, _, rng in self.graph.triples((s, RDFS.range, None)):\n+ literal = ((unicode(rng).startswith(\n+ u\"http://www.w3.org/2001/XMLSchema#\") and\n+ not unicode(rng) == u\"http://www.w3.org/2001/XMLSchema#anyURI\")\n+ or unicode(rng) ==\n+ u\"http://www.w3.org/2000/01/rdf-schema#Literal\")\n if not literal:\n- self.url_fields.add(str(s))\n- self.foreign_properties.add(str(s))\n+ self.url_fields.add(unicode(s))\n+ self.foreign_properties.add(s)\n \n- def add_namespaces(self, ns):\n+ def add_namespaces(self, ns): # type: (Dict[unicode, unicode]) -> None\n self.vocab.update(ns)\n \n def add_schemas(self, ns, base_url):\n+ # type: (Union[List[unicode], unicode], unicode) -> None\n for sch in aslist(ns):\n- try:\n- self.graph.parse(urlparse.urljoin(base_url, sch), format=\"xml\")\n- except xml.sax.SAXParseException:\n- self.graph.parse(urlparse.urljoin(base_url, sch), format=\"turtle\")\n-\n- for s, _, _ in self.graph.triples( (None, RDF.type, RDF.Property) ):\n+ for fmt in ['xml', 'turtle', 'rdfa']:\n+ try:\n+ self.graph.parse(urlparse.urljoin(base_url, sch),\n+ format=fmt)\n+ break\n+ except xml.sax.SAXParseException: # type: ignore\n+ pass\n+ except TypeError:\n+ pass\n+ except BadSyntax:\n+ pass\n+\n+ for s, _, _ in self.graph.triples((None, RDF.type, RDF.Property)):\n self._add_properties(s)\n- for s, _, o in self.graph.triples( (None, RDFS.subPropertyOf, None) ):\n+ for s, _, o in self.graph.triples((None, RDFS.subPropertyOf, None)):\n self._add_properties(s)\n self._add_properties(o)\n- for s, _, _ in self.graph.triples( (None, RDFS.range, None) ):\n+ for s, _, _ in self.graph.triples((None, RDFS.range, None)):\n self._add_properties(s)\n- for s, _, _ in self.graph.triples( (None, RDF.type, OWL.ObjectProperty) ):\n+ for s, _, _ in self.graph.triples((None, RDF.type, OWL.ObjectProperty)):\n self._add_properties(s)\n \n- for s, _, _ in self.graph.triples( (None, None, None) ):\n- self.idx[str(s)] = True\n-\n+ for s, _, _ in self.graph.triples((None, None, None)):\n+ self.idx[unicode(s)] = None\n \n def add_context(self, newcontext, baseuri=\"\"):\n+ # type: (Loader.ContextType, unicode) -> None\n if self.vocab:\n- raise validate.ValidationException(\"Refreshing context that already has stuff in it\")\n+ raise validate.ValidationException(\n+ \"Refreshing context that already has stuff in it\")\n \n self.url_fields = set()\n+ self.scoped_ref_fields = {}\n self.vocab_fields = set()\n self.identifiers = set()\n self.identity_links = set()\n@@ -175,39 +206,45 @@ def add_context(self, newcontext, baseuri=\"\"):\n self.mapPredicate = {}\n self.vocab = {}\n self.rvocab = {}\n+ self.type_dsl_fields = set()\n \n- self.ctx.update(_copy_dict_without_key(newcontext, \"@context\"))\n+ self.ctx.update(_copy_dict_without_key(newcontext, u\"@context\"))\n \n _logger.debug(\"ctx is %s\", self.ctx)\n \n- for c in self.ctx:\n- if self.ctx[c] == \"@id\":\n- self.identifiers.add(c)\n- self.identity_links.add(c)\n- elif isinstance(self.ctx[c], dict) and self.ctx[c].get(\"@type\") == \"@id\":\n- self.url_fields.add(c)\n- if self.ctx[c].get(\"identity\", False):\n- self.identity_links.add(c)\n- elif isinstance(self.ctx[c], dict) and self.ctx[c].get(\"@type\") == \"@vocab\":\n- self.url_fields.add(c)\n- self.vocab_fields.add(c)\n-\n- if isinstance(self.ctx[c], dict) and self.ctx[c].get(\"noLinkCheck\"):\n- self.nolinkcheck.add(c)\n-\n- if isinstance(self.ctx[c], dict) and self.ctx[c].get(\"mapSubject\"):\n- self.idmap[c] = self.ctx[c][\"mapSubject\"]\n-\n- if isinstance(self.ctx[c], dict) and self.ctx[c].get(\"mapPredicate\"):\n- self.mapPredicate[c] = self.ctx[c][\"mapPredicate\"]\n-\n- if isinstance(self.ctx[c], dict) and \"@id\" in self.ctx[c]:\n- self.vocab[c] = self.ctx[c][\"@id\"]\n- elif isinstance(self.ctx[c], basestring):\n- self.vocab[c] = self.ctx[c]\n-\n- for k,v in self.vocab.items():\n- self.rvocab[self.expand_url(v, \"\", scoped=False)] = k\n+ for key, value in self.ctx.items():\n+ if value == u\"@id\":\n+ self.identifiers.add(key)\n+ self.identity_links.add(key)\n+ elif isinstance(value, dict) and value.get(u\"@type\") == u\"@id\":\n+ self.url_fields.add(key)\n+ if u\"refScope\" in value:\n+ self.scoped_ref_fields[key] = value[u\"refScope\"]\n+ if value.get(u\"identity\", False):\n+ self.identity_links.add(key)\n+ elif isinstance(value, dict) and value.get(u\"@type\") == u\"@vocab\":\n+ self.url_fields.add(key)\n+ self.vocab_fields.add(key)\n+ if u\"refScope\" in value:\n+ self.scoped_ref_fields[key] = value[u\"refScope\"]\n+ if value.get(u\"typeDSL\"):\n+ self.type_dsl_fields.add(key)\n+ if isinstance(value, dict) and value.get(u\"noLinkCheck\"):\n+ self.nolinkcheck.add(key)\n+\n+ if isinstance(value, dict) and value.get(u\"mapSubject\"):\n+ self.idmap[key] = value[u\"mapSubject\"]\n+\n+ if isinstance(value, dict) and value.get(u\"mapPredicate\"):\n+ self.mapPredicate[key] = value[u\"mapPredicate\"]\n+\n+ if isinstance(value, dict) and u\"@id\" in value:\n+ self.vocab[key] = value[u\"@id\"]\n+ elif isinstance(value, basestring):\n+ self.vocab[key] = value\n+\n+ for k, v in self.vocab.items():\n+ self.rvocab[self.expand_url(v, u\"\", scoped_id=False)] = k\n \n _logger.debug(\"identifiers is %s\", self.identifiers)\n _logger.debug(\"identity_links is %s\", self.identity_links)\n@@ -215,29 +252,31 @@ def add_context(self, newcontext, baseuri=\"\"):\n _logger.debug(\"vocab_fields is %s\", self.vocab_fields)\n _logger.debug(\"vocab is %s\", self.vocab)\n \n+ def resolve_ref(self, ref, base_url=None, checklinks=True):\n+ # type: (Union[Dict[unicode, Any], unicode], unicode, bool) -> Tuple[Union[List, Dict[unicode, Any], unicode], Dict[unicode, Any]]\n+ base_url = base_url or u'file://%s/' % os.path.abspath('.')\n \n- def resolve_ref(self, ref, base_url=None):\n- base_url = base_url or 'file://%s/' % os.path.abspath('.')\n-\n- obj = None\n+ obj = None # type: Dict[unicode, Any]\n inc = False\n \n # If `ref` is a dict, look for special directives.\n if isinstance(ref, dict):\n obj = ref\n- if \"$import\" in ref:\n+ if u\"$import\" in ref:\n if len(obj) == 1:\n- ref = obj[\"$import\"]\n+ ref = obj[u\"$import\"]\n obj = None\n else:\n- raise ValueError(\"'$import' must be the only field in %s\" % (str(obj)))\n- elif \"$include\" in obj:\n+ raise ValueError(\n+ \"'$import' must be the only field in %s\" % (str(obj)))\n+ elif u\"$include\" in obj:\n if len(obj) == 1:\n- ref = obj[\"$include\"]\n+ ref = obj[u\"$include\"]\n inc = True\n obj = None\n else:\n- raise ValueError(\"'$include' must be the only field in %s\" % (str(obj)))\n+ raise ValueError(\n+ \"'$include' must be the only field in %s\" % (str(obj)))\n else:\n ref = None\n for identifier in self.identifiers:\n@@ -245,12 +284,13 @@ def resolve_ref(self, ref, base_url=None):\n ref = obj[identifier]\n break\n if not ref:\n- raise ValueError(\"Object `%s` does not have identifier field in %s\" % (obj, self.identifiers))\n+ raise ValueError(\n+ \"Object `%s` does not have identifier field in %s\" % (obj, self.identifiers))\n \n- if not isinstance(ref, basestring):\n+ if not isinstance(ref, (str, unicode)):\n raise ValueError(\"Must be string: `%s`\" % str(ref))\n \n- url = self.expand_url(ref, base_url, scoped=(obj is not None))\n+ url = self.expand_url(ref, base_url, scoped_id=(obj is not None))\n \n # Has this reference been loaded already?\n if url in self.idx:\n@@ -260,6 +300,7 @@ def resolve_ref(self, ref, base_url=None):\n if inc:\n return self.fetch_text(url), {}\n \n+ doc = None\n if obj:\n for identifier in self.identifiers:\n obj[identifier] = url\n@@ -268,136 +309,242 @@ def resolve_ref(self, ref, base_url=None):\n # Load structured document\n doc_url, frg = urlparse.urldefrag(url)\n if doc_url in self.idx:\n- raise validate.ValidationException(\"Reference `#%s` not found in file `%s`.\" % (frg, doc_url))\n- obj = self.fetch(doc_url)\n+ raise validate.ValidationException(\n+ \"Reference `#%s` not found in file `%s`.\" % (frg, doc_url))\n+ doc = self.fetch(doc_url)\n \n # Recursively expand urls and resolve directives\n- obj, metadata = self.resolve_all(obj, doc_url)\n+ resolved_obj, metadata = self.resolve_all(\n+ doc if doc else obj, doc_url, checklinks=checklinks)\n \n- # Requested reference should be in the index now, otherwise it's a bad reference\n+ # Requested reference should be in the index now, otherwise it's a bad\n+ # reference\n if url is not None:\n if url in self.idx:\n- obj = self.idx[url]\n+ resolved_obj = self.idx[url]\n else:\n- raise RuntimeError(\"Reference `%s` is not in the index. Index contains:\\n %s\" % (url, \"\\n \".join(self.idx)))\n+ raise RuntimeError(\"Reference `%s` is not in the index. \"\n+ \"Index contains:\\n %s\" % (url, \"\\n \".join(self.idx)))\n \n- try:\n- if \"$graph\" in obj:\n- metadata = _copy_dict_without_key(obj, \"$graph\")\n- obj = obj[\"$graph\"]\n- return obj, metadata\n+ if isinstance(resolved_obj, (dict)):\n+ if u\"$graph\" in resolved_obj:\n+ metadata = _copy_dict_without_key(resolved_obj, u\"$graph\")\n+ return resolved_obj[u\"$graph\"], metadata\n else:\n- return obj, metadata\n- except TypeError:\n- return obj, metadata\n+ return resolved_obj, metadata\n+ else:\n+ return resolved_obj, metadata\n+\n+\n+ def _resolve_idmap(self, document, loader):\n+ # type: (Dict[unicode, Union[Dict[unicode, Dict[unicode, unicode]], List[Dict[unicode, Any]]]], Loader) -> None\n+ # Convert fields with mapSubject into lists\n+ # use mapPredicate if the mapped value isn't a dict.\n+ for idmapField in loader.idmap:\n+ if (idmapField in document):\n+ idmapFieldValue = document[idmapField]\n+ if (isinstance(idmapFieldValue, dict)\n+ and \"$import\" not in idmapFieldValue\n+ and \"$include\" not in idmapFieldValue):\n+ ls = []\n+ for k in sorted(idmapFieldValue.keys()):\n+ val = idmapFieldValue[k]\n+ v = None # type: Dict[unicode, Any]\n+ if not isinstance(val, dict):\n+ if idmapField in loader.mapPredicate:\n+ v = {loader.mapPredicate[idmapField]: val}\n+ else:\n+ raise validate.ValidationException(\n+ \"mapSubject '%s' value '%s' is not a dict\"\n+ \"and does not have a mapPredicate\", k, v)\n+ else:\n+ v = val\n+ v[loader.idmap[idmapField]] = k\n+ ls.append(v)\n+ document[idmapField] = ls\n \n- def resolve_all(self, document, base_url, file_base=None):\n+ typeDSLregex = re.compile(ur\"^([^[?]+)(\\[\\])?(\\?)?$\")\n+\n+ def _type_dsl(self, t):\n+ # type: (Union[unicode, Dict, List]) -> Union[unicode, Dict[unicode, unicode], List[Union[unicode, Dict[unicode, unicode]]]]\n+ if not isinstance(t, (str, unicode)):\n+ return t\n+\n+ m = Loader.typeDSLregex.match(t)\n+ if not m:\n+ return t\n+ first = m.group(1)\n+ second = third = None\n+ if m.group(2):\n+ second = {u\"type\": u\"array\",\n+ u\"items\": first}\n+ if m.group(3):\n+ third = [u\"null\", second or first]\n+ return third or second or first\n+\n+ def _resolve_type_dsl(self, document, loader):\n+ # type: (Dict[unicode, Union[unicode, Dict[unicode, unicode], List]], Loader) -> None\n+ for d in loader.type_dsl_fields:\n+ if d in document:\n+ datum = document[d]\n+ if isinstance(datum, (str, unicode)):\n+ document[d] = self._type_dsl(datum)\n+ elif isinstance(datum, list):\n+ document[d] = [self._type_dsl(t) for t in datum]\n+ datum2 = document[d]\n+ if isinstance(datum2, list):\n+ document[d] = flatten(datum2)\n+ seen = [] # type: List[unicode]\n+ uniq = []\n+ for item in document[d]:\n+ if item not in seen:\n+ uniq.append(item)\n+ seen.append(item)\n+ document[d] = uniq\n+\n+ def _resolve_identifier(self, document, loader, base_url):\n+ # type: (Dict[unicode, unicode], Loader, unicode) -> unicode\n+ # Expand identifier field (usually 'id') to resolve scope\n+ for identifer in loader.identifiers:\n+ if identifer in document:\n+ if isinstance(document[identifer], basestring):\n+ document[identifer] = loader.expand_url(\n+ document[identifer], base_url, scoped_id=True)\n+ if (document[identifer] not in loader.idx\n+ or isinstance(\n+ loader.idx[document[identifer]], basestring)):\n+ loader.idx[document[identifer]] = document\n+ base_url = document[identifer]\n+ else:\n+ raise validate.ValidationException(\n+ \"identifier field '%s' must be a string\"\n+ % (document[identifer]))\n+ return base_url\n+\n+ def _resolve_identity(self, document, loader, base_url):\n+ # type: (Dict[unicode, List[unicode]], Loader, unicode) -> None\n+ # Resolve scope for identity fields (fields where the value is the\n+ # identity of a standalone node, such as enum symbols)\n+ for identifer in loader.identity_links:\n+ if identifer in document and isinstance(document[identifer], list):\n+ for n, v in enumerate(document[identifer]):\n+ if isinstance(document[identifer][n], basestring):\n+ document[identifer][n] = loader.expand_url(\n+ document[identifer][n], base_url, scoped_id=True)\n+ if document[identifer][n] not in loader.idx:\n+ loader.idx[document[identifer][\n+ n]] = document[identifer][n]\n+\n+ def _normalize_fields(self, document, loader):\n+ # type: (Dict[unicode, unicode], Loader) -> None\n+ # Normalize fields which are prefixed or full URIn to vocabulary terms\n+ for d in document:\n+ d2 = loader.expand_url(d, u\"\", scoped_id=False, vocab_term=True)\n+ if d != d2:\n+ document[d2] = document[d]\n+ del document[d]\n+\n+ def _resolve_uris(self, document, loader, base_url):\n+ # type: (Dict[unicode, Union[unicode, List[unicode]]], Loader, unicode) -> None\n+ # Resolve remaining URLs based on document base\n+ for d in loader.url_fields:\n+ if d in document:\n+ datum = document[d]\n+ if isinstance(datum, (str, unicode)):\n+ document[d] = loader.expand_url(\n+ datum, base_url, scoped_id=False,\n+ vocab_term=(d in loader.vocab_fields),\n+ scoped_ref=self.scoped_ref_fields.get(d))\n+ elif isinstance(datum, list):\n+ document[d] = [\n+ loader.expand_url(\n+ url, base_url, scoped_id=False,\n+ vocab_term=(d in loader.vocab_fields),\n+ scoped_ref=self.scoped_ref_fields.get(d))\n+ if isinstance(url, (str, unicode))\n+ else url for url in datum]\n+\n+\n+ def resolve_all(self, document, base_url, file_base=None, checklinks=True):\n+ # type: (DocumentType, unicode, unicode, bool) -> Tuple[Union[List, Dict[unicode, Any], unicode], Dict[unicode, Any]]\n loader = self\n- metadata = {} # type: Dict[str, str]\n+ metadata = {} # type: Dict[unicode, Any]\n if file_base is None:\n file_base = base_url\n \n if isinstance(document, dict):\n # Handle $import and $include\n- if ('$import' in document or '$include' in document):\n- return self.resolve_ref(document, file_base)\n+ if (u'$import' in document or u'$include' in document):\n+ return self.resolve_ref(document, base_url=file_base, checklinks=checklinks)\n elif isinstance(document, list):\n pass\n else:\n- return document, metadata\n+ return (document, metadata)\n \n- newctx = None\n+ newctx = None # type: Loader\n if isinstance(document, dict):\n # Handle $base, $profile, $namespaces, $schemas and $graph\n- if \"$base\" in document:\n- base_url = document[\"$base\"]\n+ if u\"$base\" in document:\n+ base_url = document[u\"$base\"]\n \n- if \"$profile\" in document:\n+ if u\"$profile\" in document:\n if not newctx:\n newctx = SubLoader(self)\n- prof = self.fetch(document[\"$profile\"])\n- newctx.add_namespaces(document.get(\"$namespaces\", {}), document[\"$profile\"])\n- newctx.add_schemas(document.get(\"$schemas\", []), document[\"$profile\"])\n+ prof = self.fetch(document[u\"$profile\"])\n+ newctx.add_namespaces(document.get(u\"$namespaces\", {}))\n+ newctx.add_schemas(document.get(\n+ u\"$schemas\", []), document[u\"$profile\"])\n \n- if \"$namespaces\" in document:\n+ if u\"$namespaces\" in document:\n if not newctx:\n newctx = SubLoader(self)\n- newctx.add_namespaces(document[\"$namespaces\"])\n+ newctx.add_namespaces(document[u\"$namespaces\"])\n \n- if \"$schemas\" in document:\n+ if u\"$schemas\" in document:\n if not newctx:\n newctx = SubLoader(self)\n- newctx.add_schemas(document[\"$schemas\"], file_base)\n+ newctx.add_schemas(document[u\"$schemas\"], file_base)\n \n if newctx:\n loader = newctx\n \n- if \"$graph\" in document:\n- metadata = _copy_dict_without_key(document, \"$graph\")\n- document = document[\"$graph\"]\n- metadata, _ = loader.resolve_all(metadata, base_url, file_base)\n+ if u\"$graph\" in document:\n+ metadata = _copy_dict_without_key(document, u\"$graph\")\n+ document = document[u\"$graph\"]\n+ resolved_metadata = loader.resolve_all(metadata, base_url,\n+ file_base=file_base, checklinks=False)[0]\n+ if isinstance(resolved_metadata, dict):\n+ metadata = resolved_metadata\n+ else:\n+ raise validate.ValidationException(\n+ \"Validation error, metadata must be dict: %s\"\n+ % (resolved_metadata))\n \n if isinstance(document, dict):\n- for idmapField in loader.idmap:\n- if idmapField in document and isinstance(document[idmapField], dict):\n- ls = []\n- for k,v in document[idmapField].items():\n- if not isinstance(v, dict):\n- if idmapField in loader.mapPredicate:\n- v = {loader.mapPredicate[idmapField]: v}\n- else:\n- raise validate.ValidationException(\"mapSubject '%s' value '%s' is not a dict and does not have a mapPredicate\", k, v)\n- v[loader.idmap[idmapField]] = k\n- ls.append(v)\n- document[idmapField] = ls\n-\n- for identifer in loader.identifiers:\n- if identifer in document:\n- if isinstance(document[identifer], basestring):\n- document[identifer] = loader.expand_url(document[identifer], base_url, scoped=True)\n- if document[identifer] not in loader.idx or isinstance(loader.idx[document[identifer]], basestring):\n- loader.idx[document[identifer]] = document\n- base_url = document[identifer]\n- else:\n- raise validate.ValidationException(\"identifier field '%s' must be a string\" % (document[identifer]))\n-\n- for identifer in loader.identity_links:\n- if identifer in document and isinstance(document[identifer], list):\n- for n, v in enumerate(document[identifer]):\n- document[identifer][n] = loader.expand_url(document[identifer][n], base_url, scoped=True)\n- if document[identifer][n] not in loader.idx:\n- loader.idx[document[identifer][n]] = document[identifer][n]\n- #else:\n- # raise validate.ValidationException(\"identity field '%s' must be a string\" % (document[identifer]))\n-\n- for d in document:\n- d2 = loader.expand_url(d, \"\", scoped=False, vocab_term=True)\n- if d != d2:\n- document[d2] = document[d]\n- del document[d]\n-\n- for d in loader.url_fields:\n- if d in document:\n- if isinstance(document[d], basestring):\n- document[d] = loader.expand_url(document[d], base_url, scoped=False, vocab_term=(d in loader.vocab_fields))\n- elif isinstance(document[d], list):\n- document[d] = [loader.expand_url(url, base_url, scoped=False, vocab_term=(d in loader.vocab_fields)) if isinstance(url, basestring) else url for url in document[d] ]\n+ self._normalize_fields(document, loader)\n+ self._resolve_idmap(document, loader)\n+ self._resolve_type_dsl(document, loader)\n+ base_url = self._resolve_identifier(document, loader, base_url)\n+ self._resolve_identity(document, loader, base_url)\n+ self._resolve_uris(document, loader, base_url)\n \n try:\n for key, val in document.items():\n- document[key], _ = loader.resolve_all(val, base_url, file_base)\n+ document[key], _ = loader.resolve_all(\n+ val, base_url, file_base=file_base, checklinks=False)\n except validate.ValidationException as v:\n _logger.debug(\"loader is %s\", id(loader))\n- raise validate.ValidationException(\"(%s) (%s) Validation error in field %s:\\n%s\" % (id(loader), file_base, key, validate.indent(str(v))))\n+ raise validate.ValidationException(\"(%s) (%s) Validation error in field %s:\\n%s\" % (\n+ id(loader), file_base, key, validate.indent(str(v))))\n \n elif isinstance(document, list):\n i = 0\n try:\n while i < len(document):\n val = document[i]\n- if isinstance(val, dict) and \"$import\" in val:\n- l, _ = loader.resolve_ref(val, file_base)\n- if isinstance(l, list):\n+ if isinstance(val, dict) and u\"$import\" in val:\n+ l, _ = loader.resolve_ref(val, base_url=file_base, checklinks=False)\n+ if isinstance(l, list): # never true?\n del document[i]\n for item in aslist(l):\n document.insert(i, item)\n@@ -406,27 +553,34 @@ def resolve_all(self, document, base_url, file_base=None):\n document[i] = l\n i += 1\n else:\n- document[i], _ = loader.resolve_all(val, base_url, file_base)\n+ document[i], _ = loader.resolve_all(\n+ val, base_url, file_base=file_base, checklinks=False)\n i += 1\n except validate.ValidationException as v:\n- raise validate.ValidationException(\"(%s) (%s) Validation error in position %i:\\n%s\" % (id(loader), file_base, i, validate.indent(str(v))))\n+ raise validate.ValidationException(\"(%s) (%s) Validation error in position %i:\\n%s\" % (\n+ id(loader), file_base, i, validate.indent(str(v))))\n \n for identifer in loader.identity_links:\n if identifer in metadata:\n- if isinstance(metadata[identifer], basestring):\n- metadata[identifer] = loader.expand_url(metadata[identifer], base_url, scoped=True)\n+ if isinstance(metadata[identifer], (str, unicode)):\n+ metadata[identifer] = loader.expand_url(\n+ metadata[identifer], base_url, scoped_id=True)\n loader.idx[metadata[identifer]] = document\n \n+ if checklinks:\n+ document = self.validate_links(document, u\"\")\n+\n return document, metadata\n \n def fetch_text(self, url):\n+ # type: (unicode) -> unicode\n if url in self.cache:\n return self.cache[url]\n \n split = urlparse.urlsplit(url)\n scheme, path = split.scheme, split.path\n \n- if scheme in ['http', 'https'] and requests:\n+ if scheme in [u'http', u'https'] and requests:\n try:\n resp = requests.get(url)\n resp.raise_for_status()\n@@ -446,18 +600,18 @@ def fetch_text(self, url):\n else:\n raise ValueError('Unsupported scheme in url: %s' % url)\n \n- def fetch(self, url):\n+ def fetch(self, url): # type: (unicode) -> Any\n if url in self.idx:\n return self.idx[url]\n try:\n text = self.fetch_text(url)\n if isinstance(text, bytes):\n- text = StringIO(text.decode('utf-8'))\n+ textIO = StringIO(text.decode('utf-8'))\n else:\n- text = StringIO(text)\n- text.name = url\n- result = yaml.load(text)\n- except yaml.parser.ParserError as e:\n+ textIO = StringIO(text)\n+ textIO.name = url # type: ignore\n+ result = yaml.load(textIO, Loader=SafeLoader)\n+ except yaml.parser.ParserError as e: # type: ignore\n raise validate.ValidationException(\"Syntax error %s\" % (e))\n if isinstance(result, dict) and self.identifiers:\n for identifier in self.identifiers:\n@@ -468,58 +622,97 @@ def fetch(self, url):\n self.idx[url] = result\n return result\n \n- def check_file(self, fn):\n+ def check_file(self, fn): # type: (unicode) -> bool\n if fn.startswith(\"file://\"):\n u = urlparse.urlsplit(fn)\n return os.path.exists(u.path)\n else:\n return False\n \n- def validate_link(self, field, link):\n+ FieldType = TypeVar('FieldType', unicode, List[unicode], Dict[unicode, Any])\n+\n+ def validate_scoped(self, field, link, docid):\n+ # type: (unicode, unicode, unicode) -> unicode\n+ split = urlparse.urlsplit(docid)\n+ sp = split.fragment.split(u\"/\")\n+ n = self.scoped_ref_fields[field]\n+ while n > 0 and len(sp) > 0:\n+ sp.pop()\n+ n -= 1\n+ tried = []\n+ while True:\n+ sp.append(link)\n+ url = urlparse.urlunsplit((\n+ split.scheme, split.netloc, split.path, split.query,\n+ u\"/\".join(sp)))\n+ tried.append(url)\n+ if url in self.idx:\n+ return url\n+ sp.pop()\n+ if len(sp) == 0:\n+ break\n+ sp.pop()\n+ raise validate.ValidationException(\n+ \"Field `%s` contains undefined reference to `%s`, tried %s\" % (field, link, tried))\n+\n+ def validate_link(self, field, link, docid):\n+ # type: (unicode, FieldType, unicode) -> FieldType\n if field in self.nolinkcheck:\n- return True\n- if isinstance(link, basestring):\n+ return link\n+ if isinstance(link, (str, unicode)):\n if field in self.vocab_fields:\n if link not in self.vocab and link not in self.idx and link not in self.rvocab:\n- if not self.check_file(link):\n- raise validate.ValidationException(\"Field `%s` contains undefined reference to `%s`\" % (field, link))\n+ if field in self.scoped_ref_fields:\n+ return self.validate_scoped(field, link, docid)\n+ elif not self.check_file(link):\n+ raise validate.ValidationException(\n+ \"Field `%s` contains undefined reference to `%s`\" % (field, link))\n elif link not in self.idx and link not in self.rvocab:\n- if not self.check_file(link):\n- raise validate.ValidationException(\"Field `%s` contains undefined reference to `%s`\" % (field, link))\n+ if field in self.scoped_ref_fields:\n+ return self.validate_scoped(field, link, docid)\n+ elif not self.check_file(link):\n+ raise validate.ValidationException(\n+ \"Field `%s` contains undefined reference to `%s`\" % (field, link))\n elif isinstance(link, list):\n errors = []\n- for i in link:\n+ for n, i in enumerate(link):\n try:\n- self.validate_link(field, i)\n+ link[n] = self.validate_link(field, i, docid)\n except validate.ValidationException as v:\n errors.append(v)\n if errors:\n- raise validate.ValidationException(\"\\n\".join([str(e) for e in errors]))\n+ raise validate.ValidationException(\n+ \"\\n\".join([str(e) for e in errors]))\n elif isinstance(link, dict):\n- self.validate_links(link)\n- return True\n+ self.validate_links(link, docid)\n+ else:\n+ raise validate.ValidationException(\"Link must be a str, unicode, \"\n+ \"list, or a dict.\")\n+ return link\n \n- def getid(self, d):\n+ def getid(self, d): # type: (Any) -> unicode\n if isinstance(d, dict):\n for i in self.identifiers:\n if i in d:\n- if isinstance(d[i], basestring):\n+ if isinstance(d[i], (str, unicode)):\n return d[i]\n return None\n \n- def validate_links(self, document):\n+ def validate_links(self, document, base_url):\n+ # type: (DocumentType, unicode) -> DocumentType\n docid = self.getid(document)\n- if docid is None:\n- docid = \"\"\n+ if not docid:\n+ docid = base_url\n \n errors = []\n+ iterator = None # type: Any\n if isinstance(document, list):\n iterator = enumerate(document)\n elif isinstance(document, dict):\n try:\n for d in self.url_fields:\n- if d not in self.identity_links and d in document:\n- self.validate_link(d, document[d])\n+ if d in document and d not in self.identity_links:\n+ document[d] = self.validate_link(d, document[d], docid)\n except validate.ValidationException as v:\n errors.append(v)\n if hasattr(document, \"iteritems\"):\n@@ -527,31 +720,36 @@ def validate_links(self, document):\n else:\n iterator = document.items()\n else:\n- return\n+ return document\n \n for key, val in iterator:\n try:\n- self.validate_links(val)\n+ document[key] = self.validate_links(val, docid) # type: ignore\n except validate.ValidationException as v:\n if key not in self.nolinkcheck:\n- docid = self.getid(val)\n- if docid:\n- errors.append(validate.ValidationException(\"While checking object `%s`\\n%s\" % (docid, validate.indent(str(v)))))\n+ docid2 = self.getid(val)\n+ if docid2:\n+ errors.append(validate.ValidationException(\n+ \"While checking object `%s`\\n%s\" % (docid2, validate.indent(str(v)))))\n else:\n if isinstance(key, basestring):\n- errors.append(validate.ValidationException(\"While checking field `%s`\\n%s\" % (key, validate.indent(str(v)))))\n+ errors.append(validate.ValidationException(\n+ \"While checking field `%s`\\n%s\" % (key, validate.indent(str(v)))))\n else:\n- errors.append(validate.ValidationException(\"While checking position %s\\n%s\" % (key, validate.indent(str(v)))))\n+ errors.append(validate.ValidationException(\n+ \"While checking position %s\\n%s\" % (key, validate.indent(str(v)))))\n \n if errors:\n if len(errors) > 1:\n- raise validate.ValidationException(\"\\n\".join([str(e) for e in errors]))\n+ raise validate.ValidationException(\n+ \"\\n\".join([str(e) for e in errors]))\n else:\n raise errors[0]\n- return\n+ return document\n \n \n def _copy_dict_without_key(from_dict, filtered_key):\n+ # type: (Dict, Any) -> Dict\n new_dict = {}\n for key, value in from_dict.items():\n if key != filtered_key:\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/schema.py b/cwltool/schemas/draft-4/salad/schema_salad/schema.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/schema.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/schema.py\n@@ -4,49 +4,51 @@\n import sys\n import pprint\n from pkg_resources import resource_stream\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 avro.schema\n from . import validate\n import json\n-try:\n- import urlparse\n- AvroSchemaFromJSONData=avro.schema.make_avsc_object\n-except ImportError:\n- import urllib.parse as urlparse\n- basestring=str\n- AvroSchemaFromJSONData=avro.schema.SchemaFromJSONData\n+import urlparse\n+AvroSchemaFromJSONData = avro.schema.make_avsc_object\n+# AvroSchemaFromJSONData=avro.schema.SchemaFromJSONData\n from . import ref_resolver\n from .flatten import flatten\n import logging\n from .aslist import aslist\n from . import jsonld_context\n-if sys.version_info >= (2,7):\n- import typing\n+from typing import Any, AnyStr, cast, Dict, List, Tuple, TypeVar, Union\n \n _logger = logging.getLogger(\"salad\")\n \n salad_files = ('metaschema.yml',\n- 'salad.md',\n- 'field_name.yml',\n- 'import_include.md',\n- 'link_res.yml',\n- 'ident_res.yml',\n- 'vocab_res.yml',\n- 'vocab_res.yml',\n- 'field_name_schema.yml',\n- 'field_name_src.yml',\n- 'field_name_proc.yml',\n- 'ident_res_schema.yml',\n- 'ident_res_src.yml',\n- 'ident_res_proc.yml',\n- 'link_res_schema.yml',\n- 'link_res_src.yml',\n- 'link_res_proc.yml',\n- 'vocab_res_schema.yml',\n- 'vocab_res_src.yml',\n- 'vocab_res_proc.yml')\n+ 'metaschema_base.yml',\n+ 'salad.md',\n+ 'field_name.yml',\n+ 'import_include.md',\n+ 'link_res.yml',\n+ 'ident_res.yml',\n+ 'vocab_res.yml',\n+ 'vocab_res.yml',\n+ 'field_name_schema.yml',\n+ 'field_name_src.yml',\n+ 'field_name_proc.yml',\n+ 'ident_res_schema.yml',\n+ 'ident_res_src.yml',\n+ 'ident_res_proc.yml',\n+ 'link_res_schema.yml',\n+ 'link_res_src.yml',\n+ 'link_res_proc.yml',\n+ 'vocab_res_schema.yml',\n+ 'vocab_res_src.yml',\n+ 'vocab_res_proc.yml')\n+\n \n def get_metaschema():\n+ # type: () -> Tuple[avro.schema.Names, List[Dict[unicode, Any]], ref_resolver.Loader]\n loader = ref_resolver.Loader({\n \"Any\": \"https://w3id.org/cwl/salad#Any\",\n \"ArraySchema\": \"https://w3id.org/cwl/salad#ArraySchema\",\n@@ -78,21 +80,22 @@ def get_metaschema():\n \"@id\": \"https://w3id.org/cwl/salad#docAfter\",\n \"@type\": \"@id\"\n },\n- \"docParent\": {\n- \"@id\": \"https://w3id.org/cwl/salad#docParent\",\n- \"@type\": \"@id\"\n- },\n \"docChild\": {\n \"@id\": \"https://w3id.org/cwl/salad#docChild\",\n \"@type\": \"@id\"\n },\n+ \"docParent\": {\n+ \"@id\": \"https://w3id.org/cwl/salad#docParent\",\n+ \"@type\": \"@id\"\n+ },\n \"documentRoot\": \"https://w3id.org/cwl/salad#SchemaDefinedType/documentRoot\",\n \"documentation\": \"https://w3id.org/cwl/salad#documentation\",\n \"double\": \"http://www.w3.org/2001/XMLSchema#double\",\n \"enum\": \"https://w3id.org/cwl/salad#enum\",\n \"extends\": {\n \"@id\": \"https://w3id.org/cwl/salad#extends\",\n- \"@type\": \"@id\"\n+ \"@type\": \"@id\",\n+ \"refScope\": 1\n },\n \"fields\": \"sld:fields\",\n \"float\": \"http://www.w3.org/2001/XMLSchema#float\",\n@@ -100,16 +103,20 @@ def get_metaschema():\n \"int\": \"http://www.w3.org/2001/XMLSchema#int\",\n \"items\": {\n \"@id\": \"https://w3id.org/cwl/salad#items\",\n- \"@type\": \"@vocab\"\n+ \"@type\": \"@vocab\",\n+ \"refScope\": 2\n },\n \"jsonldPredicate\": \"sld:jsonldPredicate\",\n \"long\": \"http://www.w3.org/2001/XMLSchema#long\",\n+ \"mapPredicate\": \"https://w3id.org/cwl/salad#JsonldPredicate/mapPredicate\",\n+ \"mapSubject\": \"https://w3id.org/cwl/salad#JsonldPredicate/mapSubject\",\n \"name\": \"@id\",\n \"noLinkCheck\": \"https://w3id.org/cwl/salad#JsonldPredicate/noLinkCheck\",\n \"null\": \"https://w3id.org/cwl/salad#null\",\n \"rdf\": \"http://www.w3.org/1999/02/22-rdf-syntax-ns#\",\n \"rdfs\": \"http://www.w3.org/2000/01/rdf-schema#\",\n \"record\": \"https://w3id.org/cwl/salad#record\",\n+ \"refScope\": \"https://w3id.org/cwl/salad#JsonldPredicate/refScope\",\n \"sld\": \"https://w3id.org/cwl/salad#\",\n \"specialize\": \"https://w3id.org/cwl/salad#SaladRecordSchema/specialize\",\n \"specializeFrom\": {\n@@ -128,8 +135,11 @@ def get_metaschema():\n },\n \"type\": {\n \"@id\": \"https://w3id.org/cwl/salad#type\",\n- \"@type\": \"@vocab\"\n+ \"@type\": \"@vocab\",\n+ \"refScope\": 2,\n+ \"typeDSL\": True\n },\n+ \"typeDSL\": \"https://w3id.org/cwl/salad#JsonldPredicate/typeDSL\",\n \"xsd\": \"http://www.w3.org/2001/XMLSchema#\"\n })\n \n@@ -142,62 +152,74 @@ def get_metaschema():\n loader.cache[\"https://w3id.org/cwl/salad\"] = rs.read()\n rs.close()\n \n- j = yaml.load(loader.cache[\"https://w3id.org/cwl/salad\"])\n+ j = yaml.load(loader.cache[\"https://w3id.org/cwl/salad\"],\n+ Loader=SafeLoader)\n j, _ = loader.resolve_all(j, \"https://w3id.org/cwl/salad#\")\n \n- #pprint.pprint(j)\n+ # pprint.pprint(j)\n \n (sch_names, sch_obj) = make_avro_schema(j, loader)\n if isinstance(sch_names, Exception):\n- _logger.error(\"Metaschema error, avro was:\\n%s\", json.dumps(sch_obj, indent=4))\n+ _logger.error(\"Metaschema error, avro was:\\n%s\",\n+ json.dumps(sch_obj, indent=4))\n raise sch_names\n validate_doc(sch_names, j, loader, strict=True)\n return (sch_names, j, loader)\n \n+\n def load_schema(schema_ref, cache=None):\n+ # type: (Union[unicode, Dict[unicode, Any]], Dict) -> Tuple[ref_resolver.Loader, Union[avro.schema.Names, avro.schema.SchemaParseException], Dict[unicode, Any], ref_resolver.Loader]\n metaschema_names, metaschema_doc, metaschema_loader = get_metaschema()\n if cache is not None:\n metaschema_loader.cache = cache\n schema_doc, schema_metadata = metaschema_loader.resolve_ref(schema_ref, \"\")\n \n+ if not isinstance(schema_doc, list):\n+ raise ValueError(\"Schema reference must resolve to a list.\")\n+\n validate_doc(metaschema_names, schema_doc, metaschema_loader, True)\n metactx = schema_metadata.get(\"@context\", {})\n metactx.update(schema_metadata.get(\"$namespaces\", {}))\n- (schema_ctx, rdfs) = jsonld_context.salad_to_jsonld_context(schema_doc, metactx)\n+ (schema_ctx, rdfs) = jsonld_context.salad_to_jsonld_context(\n+ schema_doc, metactx)\n \n # Create the loader that will be used to load the target document.\n document_loader = ref_resolver.Loader(schema_ctx, cache=cache)\n \n- # Make the Avro validation that will be used to validate the target document\n+ # Make the Avro validation that will be used to validate the target\n+ # document\n (avsc_names, avsc_obj) = make_avro_schema(schema_doc, document_loader)\n \n- return document_loader, avsc_names, schema_metadata\n+ return document_loader, avsc_names, schema_metadata, metaschema_loader\n \n def load_and_validate(document_loader, avsc_names, document, strict):\n+ # type: (ref_resolver.Loader, avro.schema.Names, Union[Dict[unicode, Any], unicode], bool) -> Tuple[Any, Dict[unicode, Any]]\n if isinstance(document, dict):\n data, metadata = document_loader.resolve_all(document, document[\"id\"])\n else:\n data, metadata = document_loader.resolve_ref(document)\n \n- document_loader.validate_links(data)\n validate_doc(avsc_names, data, document_loader, strict)\n return data, metadata\n \n-def validate_doc(schema_names, validate_doc, loader, strict):\n+\n+def validate_doc(schema_names, doc, loader, strict):\n+ # type: (avro.schema.Names, Union[Dict[unicode, Any], List[Dict[unicode, Any]], unicode], ref_resolver.Loader, bool) -> None\n has_root = False\n for r in schema_names.names.values():\n- if ((hasattr(r, 'get_prop') and r.get_prop(\"documentRoot\")) or (\n- \"documentRoot\" in r.props)):\n+ if ((hasattr(r, 'get_prop') and r.get_prop(u\"documentRoot\")) or (\n+ u\"documentRoot\" in r.props)):\n has_root = True\n break\n \n if not has_root:\n- raise validate.ValidationException(\"No document roots defined in the schema\")\n+ raise validate.ValidationException(\n+ \"No document roots defined in the schema\")\n \n- if isinstance(validate_doc, list):\n- pass\n- elif isinstance(validate_doc, dict):\n- validate_doc = [validate_doc]\n+ if isinstance(doc, list):\n+ validate_doc = doc\n+ elif isinstance(doc, dict):\n+ validate_doc = [doc]\n else:\n raise validate.ValidationException(\"Document must be dict or list\")\n \n@@ -206,30 +228,34 @@ def validate_doc(schema_names, validate_doc, loader, strict):\n errors = []\n success = False\n for r in schema_names.names.values():\n- if ((hasattr(r,\"get_prop\") and r.get_prop(\"documentRoot\")) or (\n- \"documentRoot\" in r.props)):\n+ if ((hasattr(r, \"get_prop\") and r.get_prop(u\"documentRoot\")) or (\n+ u\"documentRoot\" in r.props)):\n try:\n- validate.validate_ex(r, item, loader.identifiers, strict, foreign_properties=loader.foreign_properties)\n+ validate.validate_ex(\n+ r, item, loader.identifiers, strict, foreign_properties=loader.foreign_properties)\n success = True\n break\n except validate.ValidationException as e:\n if hasattr(r, \"get_prop\"):\n- name = r.get_prop(\"name\")\n+ name = r.get_prop(u\"name\")\n elif hasattr(r, \"name\"):\n name = r.name\n- errors.append(\"Could not validate as `%s` because\\n%s\" % (name, validate.indent(str(e), nolead=False)))\n+ errors.append(\"Could not validate as `%s` because\\n%s\" % (\n+ name, validate.indent(str(e), nolead=False)))\n if not success:\n objerr = \"Validation error at position %i\" % pos\n for ident in loader.identifiers:\n if ident in item:\n objerr = \"Validation error in object %s\" % (item[ident])\n break\n- anyerrors.append(\"%s\\n%s\" % (objerr, validate.indent(\"\\n\".join(errors))))\n+ anyerrors.append(\"%s\\n%s\" %\n+ (objerr, validate.indent(\"\\n\".join(errors))))\n if anyerrors:\n raise validate.ValidationException(\"\\n\".join(anyerrors))\n \n \n def replace_type(items, spec, loader, found):\n+ # type: (Any, Dict[unicode, Any], ref_resolver.Loader, Set[unicode]) -> Any\n \"\"\" Go through and replace types in the 'spec' mapping\"\"\"\n \n items = copy.deepcopy(items)\n@@ -252,11 +278,12 @@ def replace_type(items, spec, loader, found):\n elif isinstance(items, list):\n # recursively transform list\n return [replace_type(i, spec, loader, found) for i in items]\n- elif isinstance(items, basestring):\n+ elif isinstance(items, (str, unicode)):\n # found a string which is a symbol corresponding to a type.\n replace_with = None\n if items in loader.vocab:\n- # If it's a vocabulary term, first expand it to its fully qualified URI\n+ # If it's a vocabulary term, first expand it to its fully qualified\n+ # URI\n items = loader.vocab[items]\n \n if items in spec:\n@@ -267,16 +294,20 @@ def replace_type(items, spec, loader, found):\n return replace_type(replace_with, spec, loader, found)\n return items\n \n-def avro_name(url):\n+\n+def avro_name(url): # type: (AnyStr) -> AnyStr\n doc_url, frg = urlparse.urldefrag(url)\n if frg:\n if '/' in frg:\n- return frg[frg.rindex('/')+1:]\n+ return frg[frg.rindex('/') + 1:]\n else:\n return frg\n return url\n \n+Avro = TypeVar('Avro', Dict[unicode, Any], List[Any], unicode)\n+\n def make_valid_avro(items, alltypes, found, union=False):\n+ # type: (Avro, Dict[unicode, Dict[unicode, Any]], Set[unicode], bool) -> Union[Avro, Dict]\n items = copy.deepcopy(items)\n if isinstance(items, dict):\n if items.get(\"name\"):\n@@ -284,10 +315,11 @@ def make_valid_avro(items, alltypes, found, union=False):\n \n if \"type\" in items and items[\"type\"] in (\"https://w3id.org/cwl/salad#record\", \"https://w3id.org/cwl/salad#enum\", \"record\", \"enum\"):\n if (hasattr(items, \"get\") and items.get(\"abstract\")) or (\"abstract\"\n- in items):\n+ in items):\n return items\n if not items.get(\"name\"):\n- raise Exception(\"Named schemas must have a non-empty name: %s\" % items)\n+ raise Exception(\n+ \"Named schemas must have a non-empty name: %s\" % items)\n \n if items[\"name\"] in found:\n return items[\"name\"]\n@@ -295,7 +327,8 @@ def make_valid_avro(items, alltypes, found, union=False):\n found.add(items[\"name\"])\n for n in (\"type\", \"items\", \"values\", \"fields\"):\n if n in items:\n- items[n] = make_valid_avro(items[n], alltypes, found, union=True)\n+ items[n] = make_valid_avro(\n+ items[n], alltypes, found, union=True)\n if \"symbols\" in items:\n items[\"symbols\"] = [avro_name(sym) for sym in items[\"symbols\"]]\n return items\n@@ -304,18 +337,21 @@ def make_valid_avro(items, alltypes, found, union=False):\n for i in items:\n ret.append(make_valid_avro(i, alltypes, found, union=union))\n return ret\n- if union and isinstance(items, basestring):\n+ if union and isinstance(items, (str, unicode)):\n if items in alltypes and avro_name(items) not in found:\n- return make_valid_avro(alltypes[items], alltypes, found, union=union)\n- items = avro_name(items)\n+ return cast(Dict, make_valid_avro(alltypes[items], alltypes, found,\n+ union=union))\n+ items = avro_name(items) # type: ignore\n+ # bug in mypy 0.3.1, fixed in 0.4-dev\n return items\n \n \n def extend_and_specialize(items, loader):\n+ # type: (List[Dict[unicode, Any]], ref_resolver.Loader) -> List[Dict[unicode, Any]]\n \"\"\"Apply 'extend' and 'specialize' to fully materialize derived record\n types.\"\"\"\n \n- types = {}\n+ types = {} # type: Dict[unicode, Any]\n for t in items:\n types[t[\"name\"]] = t\n n = []\n@@ -323,22 +359,24 @@ def extend_and_specialize(items, loader):\n for t in items:\n t = copy.deepcopy(t)\n if \"extends\" in t:\n- spec = {}\n+ spec = {} # type: Dict[unicode, unicode]\n if \"specialize\" in t:\n for sp in aslist(t[\"specialize\"]):\n spec[sp[\"specializeFrom\"]] = sp[\"specializeTo\"]\n \n- exfields = [] # type: List[str]\n- exsym = [] # type: List[str]\n+ exfields = [] # type: List[unicode]\n+ exsym = [] # type: List[unicode]\n for ex in aslist(t[\"extends\"]):\n if ex not in types:\n- raise Exception(\"Extends %s in %s refers to invalid base type\" % (t[\"extends\"], t[\"name\"]))\n+ raise Exception(\"Extends %s in %s refers to invalid base type\" % (\n+ t[\"extends\"], t[\"name\"]))\n \n basetype = copy.deepcopy(types[ex])\n \n if t[\"type\"] == \"record\":\n if spec:\n- basetype[\"fields\"] = replace_type(basetype.get(\"fields\", []), spec, loader, set())\n+ basetype[\"fields\"] = replace_type(\n+ basetype.get(\"fields\", []), spec, loader, set())\n \n for f in basetype.get(\"fields\", []):\n if \"inherited_from\" not in f:\n@@ -352,19 +390,13 @@ def extend_and_specialize(items, loader):\n exfields.extend(t.get(\"fields\", []))\n t[\"fields\"] = exfields\n \n- fieldnames = set() # type: Set[str]\n+ fieldnames = set() # type: Set[unicode]\n for field in t[\"fields\"]:\n if field[\"name\"] in fieldnames:\n- raise validate.ValidationException(\"Field name %s appears twice in %s\" % (field[\"name\"], t[\"name\"]))\n+ raise validate.ValidationException(\n+ \"Field name %s appears twice in %s\" % (field[\"name\"], t[\"name\"]))\n else:\n fieldnames.add(field[\"name\"])\n-\n- for y in [x for x in t[\"fields\"] if x[\"name\"] == \"class\"]:\n- y[\"type\"] = {\"type\": \"enum\",\n- \"symbols\": [r[\"name\"]],\n- \"name\": r[\"name\"]+\"_class\",\n- }\n- y[\"doc\"] = \"Must be `%s` to indicate this is a %s object.\" % (r[\"name\"], r[\"name\"])\n elif t[\"type\"] == \"enum\":\n exsym.extend(t.get(\"symbols\", []))\n t[\"symbol\"] = exsym\n@@ -377,7 +409,7 @@ def extend_and_specialize(items, loader):\n for t in n:\n ex_types[t[\"name\"]] = t\n \n- extended_by = {} # type: Dict[str, str]\n+ extended_by = {} # type: Dict[unicode, unicode]\n for t in n:\n if \"extends\" in t:\n for ex in aslist(t[\"extends\"]):\n@@ -385,29 +417,34 @@ def extend_and_specialize(items, loader):\n add_dictlist(extended_by, ex, ex_types[t[\"name\"]])\n add_dictlist(extended_by, avro_name(ex), ex_types[ex])\n \n+ for t in n:\n+ if t.get(\"abstract\") and t[\"name\"] not in extended_by:\n+ raise validate.ValidationException(\"%s is abstract but missing a concrete subtype\" % t[\"name\"])\n+\n for t in n:\n if \"fields\" in t:\n t[\"fields\"] = replace_type(t[\"fields\"], extended_by, loader, set())\n \n return n\n \n-def make_avro_schema(j, loader):\n- names = avro.schema.Names()\n \n- #pprint.pprint(j)\n+def make_avro_schema(i, loader):\n+ # type: (List[Dict[unicode, Any]], ref_resolver.Loader) -> Tuple[Union[avro.schema.Names,avro.schema.SchemaParseException], List[Dict[unicode, Any]]]\n+ names = avro.schema.Names()\n \n- j = extend_and_specialize(j, loader)\n+ j = extend_and_specialize(i, loader)\n \n- name_dict = {}\n+ name_dict = {} # type: Dict[unicode, Dict[unicode, Any]]\n for t in j:\n name_dict[t[\"name\"]] = t\n j2 = make_valid_avro(j, name_dict, set())\n \n- j3 = [t for t in j2 if isinstance(t, dict) and not t.get(\"abstract\") and t.get(\"type\") != \"documentation\"]\n+ j3 = [t for t in j2 if isinstance(t, dict) and not t.get(\n+ \"abstract\") and t.get(\"type\") != \"documentation\"]\n \n try:\n AvroSchemaFromJSONData(j3, names)\n except avro.schema.SchemaParseException as e:\n- names = e\n+ return (e, j3)\n \n return (names, j3)\ndiff --git a/cwltool/schemas/draft-4/salad/schema_salad/validate.py b/cwltool/schemas/draft-4/salad/schema_salad/validate.py\n--- a/cwltool/schemas/draft-4/salad/schema_salad/validate.py\n+++ b/cwltool/schemas/draft-4/salad/schema_salad/validate.py\n@@ -1,19 +1,14 @@\n import pprint\n import avro.schema\n-import yaml\n import sys\n-try:\n- import urlparse\n-except:\n- import urllib.parse as urlparse\n- basestring=str\n-if sys.version_info >= (2,7):\n- import typing\n+import urlparse\n+from typing import Any\n \n class ValidationException(Exception):\n pass\n \n-def validate(expected_schema, datum, identifiers=[], strict=False, foreign_properties=set()):\n+def validate(expected_schema, datum, identifiers=set(), strict=False, foreign_properties=set()):\n+ # type: (avro.schema.Schema, Any, Set[unicode], bool, Set[unicode]) -> bool\n try:\n return validate_ex(expected_schema, datum, identifiers, strict=strict, foreign_properties=foreign_properties)\n except ValidationException:\n@@ -24,13 +19,13 @@ def validate(expected_schema, datum, identifiers=[], strict=False, foreign_prope\n LONG_MIN_VALUE = -(1 << 63)\n LONG_MAX_VALUE = (1 << 63) - 1\n \n-def indent(v, nolead=False):\n+def indent(v, nolead=False): # type: (str, bool) -> str\n if nolead:\n return v.splitlines()[0] + \"\\n\".join([\" \" + l for l in v.splitlines()[1:]])\n else:\n return \"\\n\".join([\" \" + l for l in v.splitlines()])\n \n-def friendly(v):\n+def friendly(v): # type: (Any) -> Any\n if isinstance(v, avro.schema.NamedSchema):\n return v.name\n if isinstance(v, avro.schema.ArraySchema):\n@@ -42,21 +37,29 @@ def friendly(v):\n else:\n return v\n \n-def multi(v, q=\"\"):\n+def multi(v, q=\"\"): # type: (str, str) -> str\n if '\\n' in v:\n return \"%s%s%s\\n\" % (q, v, q)\n else:\n return \"%s%s%s\" % (q, v, q)\n \n-def vpformat(datum):\n+def vpformat(datum): # type: (Any) -> str\n a = pprint.pformat(datum)\n if len(a) > 160:\n a = a[0:160] + \"[...]\"\n return a\n \n-def validate_ex(expected_schema, datum, identifiers=set(), strict=False, foreign_properties=set()):\n+def validate_ex(expected_schema, datum, identifiers=None, strict=False,\n+ foreign_properties=None):\n+ # type: (avro.schema.Schema, Any, Set[unicode], bool, Set[unicode]) -> bool\n \"\"\"Determine if a python datum is an instance of a schema.\"\"\"\n \n+ if not identifiers:\n+ identifiers = set()\n+\n+ if not foreign_properties:\n+ foreign_properties = set()\n+\n schema_type = expected_schema.type\n \n if schema_type == 'null':\n@@ -100,12 +103,12 @@ def validate_ex(expected_schema, datum, identifiers=set(), strict=False, foreign\n return True\n else:\n raise ValidationException(\"the value `%s` is not float or double\" % vpformat(datum))\n- elif schema_type == 'fixed':\n+ elif isinstance(expected_schema, avro.schema.FixedSchema):\n if isinstance(datum, str) and len(datum) == expected_schema.size:\n return True\n else:\n raise ValidationException(\"the value `%s` is not fixed\" % vpformat(datum))\n- elif schema_type == 'enum':\n+ elif isinstance(expected_schema, avro.schema.EnumSchema):\n if expected_schema.name == \"Any\":\n if datum is not None:\n return True\n@@ -115,7 +118,7 @@ def validate_ex(expected_schema, datum, identifiers=set(), strict=False, foreign\n return True\n else:\n raise ValidationException(\"the value `%s`\\n is not a valid symbol in enum %s, expected one of %s\" % (vpformat(datum), expected_schema.name, \"'\" + \"', '\".join(expected_schema.symbols) + \"'\"))\n- elif schema_type == 'array':\n+ elif isinstance(expected_schema, avro.schema.ArraySchema):\n if isinstance(datum, list):\n for i, d in enumerate(datum):\n try:\n@@ -125,14 +128,14 @@ def validate_ex(expected_schema, datum, identifiers=set(), strict=False, foreign\n return True\n else:\n raise ValidationException(\"the value `%s` is not a list, expected list of %s\" % (vpformat(datum), friendly(expected_schema.items)))\n- elif schema_type == 'map':\n+ elif isinstance(expected_schema, avro.schema.MapSchema):\n if (isinstance(datum, dict) and\n False not in [isinstance(k, basestring) for k in datum.keys()] and\n False not in [validate(expected_schema.values, v, strict=strict) for v in datum.values()]):\n return True\n else:\n raise ValidationException(\"`%s` is not a valid map value, expected\\n %s\" % (vpformat(datum), vpformat(expected_schema.values)))\n- elif schema_type in ['union', 'error_union']:\n+ elif isinstance(expected_schema, avro.schema.UnionSchema):\n if True in [validate(s, datum, identifiers, strict=strict) for s in expected_schema.schemas]:\n return True\n else:\n@@ -144,7 +147,7 @@ def validate_ex(expected_schema, datum, identifiers=set(), strict=False, foreign\n errors.append(str(e))\n raise ValidationException(\"the value %s is not a valid type in the union, expected one of:\\n%s\" % (multi(vpformat(datum), '`'), \"\\n\".join([\"- %s, but\\n %s\" % (friendly(expected_schema.schemas[i]), indent(multi(errors[i]))) for i in range(0, len(expected_schema.schemas))])))\n \n- elif schema_type in ['record', 'error', 'request']:\n+ elif isinstance(expected_schema, avro.schema.RecordSchema):\n if not isinstance(datum, dict):\n raise ValidationException(\"`%s`\\n is not a dict\" % vpformat(datum))\n \ndiff --git a/cwltool/schemas/draft-4/salad/setup.py b/cwltool/schemas/draft-4/salad/setup.py\n--- a/cwltool/schemas/draft-4/salad/setup.py\n+++ b/cwltool/schemas/draft-4/salad/setup.py\n@@ -24,21 +24,24 @@\n # In tox, it will cover them anyway.\n requirements = []\n \n-install_requires=[\n- 'requests',\n- 'PyYAML',\n- 'rdflib >= 4.1.0',\n- 'rdflib-jsonld >= 0.3.0',\n- 'mistune',\n- 'typing']\n+install_requires = [\n+ 'requests',\n+ 'ruamel.yaml',\n+ 'rdflib >= 4.1.0',\n+ 'rdflib-jsonld >= 0.3.0',\n+ 'mistune',\n+ 'typing']\n \n-if sys.version_info.major < 3:\n- install_requires.append(\"avro\")\n-else:\n- install_requires.append(\"avro-python3\")\n+install_requires.append(\"avro\") # TODO: remove me once cwltool is\n+# available in Debian Stable, Ubuntu 12.04 LTS\n+\n+# extras_require={ # TODO: uncomment me, same conditions as above\n+# ':python_version<\"3\"': ['avro'],\n+# ':python_version>=\"3\"': ['avro-python3']}\n+extras_require = {} # TODO: to be removed when the above is added\n \n setup(name='schema-salad',\n- version='1.9',\n+ version='1.12',\n description='Schema Annotations for Linked Avro Data (SALAD)',\n long_description=open(README).read(),\n author='Common workflow language working group',\n@@ -49,6 +52,7 @@\n packages=[\"schema_salad\"],\n package_data={'schema_salad': ['metaschema/*']},\n install_requires=install_requires,\n+ extras_require=extras_require,\n test_suite='tests',\n tests_require=[],\n entry_points={\n@@ -63,7 +67,8 @@\n \"Operating System :: MacOS :: MacOS X\",\n \"Development Status :: 4 - Beta\",\n \"Programming Language :: Python :: 2.7\",\n- \"Programming Language :: Python :: 3.3\",\n- \"Programming Language :: Python :: 3.4\",\n- \"Programming Language :: Python :: 3.5\"]\n+ #\"Programming Language :: Python :: 3.3\", # TODO: uncomment these\n+ #\"Programming Language :: Python :: 3.4\", # lines\n+ #\"Programming Language :: Python :: 3.5\"\n+ ]\n )\ndiff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/ruamel/__init__.py b/cwltool/schemas/draft-4/salad/typeshed/2.7/ruamel/__init__.py\nnew file mode 100644\ndiff --git a/cwltool/stdfsaccess.py b/cwltool/stdfsaccess.py\n--- a/cwltool/stdfsaccess.py\n+++ b/cwltool/stdfsaccess.py\n@@ -1,4 +1,4 @@\n-from typing import Any, IO\n+from typing import Any, BinaryIO\n from .pathmapper import abspath\n import glob\n import os\n@@ -6,17 +6,17 @@\n \n class StdFsAccess(object):\n \n- def __init__(self, basedir): # type: (str) -> None\n+ def __init__(self, basedir): # type: (unicode) -> None\n self.basedir = basedir\n \n- def _abs(self, p): # type: (str) -> str\n+ def _abs(self, p): # type: (unicode) -> unicode\n return abspath(p, self.basedir)\n \n- def glob(self, pattern): # type: (str) -> List[str]\n+ def glob(self, pattern): # type: (unicode) -> List[unicode]\n return glob.glob(self._abs(pattern))\n \n- def open(self, fn, mode): # type: (str, str) -> IO[Any]\n+ def open(self, fn, mode): # type: (unicode, str) -> BinaryIO\n return open(self._abs(fn), mode)\n \n- def exists(self, fn): # type: (str) -> bool\n+ def exists(self, fn): # type: (unicode) -> bool\n return os.path.exists(self._abs(fn))\ndiff --git a/cwltool/update.py b/cwltool/update.py\n--- a/cwltool/update.py\n+++ b/cwltool/update.py\n@@ -341,6 +341,25 @@ def draft3toDraft4dev1(doc, loader, baseuri):\n \"\"\"Public updater for draft-3 to draft-4.dev1.\"\"\"\n return (_draft3toDraft4dev1(doc, loader, baseuri), \"draft-4.dev1\")\n \n+def _draft4Dev1toDev2(doc, loader, baseuri):\n+ # type: (Any, Loader, str) -> Any\n+ if isinstance(doc, dict):\n+ if \"class\" in doc and doc[\"class\"] == \"Workflow\":\n+ for out in doc[\"outputs\"]:\n+ out[\"outputSource\"] = out[\"source\"]\n+ del out[\"source\"]\n+ for key, value in doc.items():\n+ doc[key] = _draft4Dev1toDev2(value, loader, baseuri)\n+ elif isinstance(doc, list):\n+ doc = [_draft4Dev1toDev2(item, loader, baseuri) for item in doc]\n+\n+ return doc\n+\n+def draft4Dev1toDev2(doc, loader, baseuri):\n+ # type: (Any, Loader, str) -> Tuple[Any, str]\n+ \"\"\"Public updater for draft-4.dev1 to draft-4.dev2.\"\"\"\n+ return (_draft4Dev1toDev2(doc, loader, baseuri), \"draft-4.dev2\")\n+\n UPDATES = {\n \"draft-2\": draft2toDraft3dev1,\n \"draft-3\": draft3toDraft4dev1\n@@ -352,13 +371,14 @@ def draft3toDraft4dev1(doc, loader, baseuri):\n \"draft-3.dev3\": draftDraft3dev3toDev4,\n \"draft-3.dev4\": draftDraft3dev4toDev5,\n \"draft-3.dev5\": draftDraft3dev5toFinal,\n- \"draft-4.dev1\": None\n+ \"draft-4.dev1\": draft4Dev1toDev2,\n+ \"draft-4.dev2\": None\n } # type: Dict[unicode, Callable[[Any, Loader, str], Tuple[Any, str]]]\n \n ALLUPDATES = UPDATES.copy()\n ALLUPDATES.update(DEVUPDATES)\n \n-LATEST = \"draft-4.dev1\"\n+LATEST = \"draft-4.dev2\"\n \n def identity(doc, loader, baseuri): # pylint: disable=unused-argument\n # type: (Any, Loader, str) -> Tuple[Any, Union[str, unicode]]\n@@ -366,19 +386,19 @@ def identity(doc, loader, baseuri): # pylint: disable=unused-argument\n return (doc, doc[\"cwlVersion\"])\n \n def checkversion(doc, metadata, enable_dev):\n- # type: (Union[List, Dict[str, Any]], Dict[str, Any], bool) -> Tuple[Dict[str, Any], Union[str, unicode]] # pylint: disable=line-too-long\n+ # type: (Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Dict[unicode, Any], bool) -> Tuple[Dict[unicode, Any], unicode] # pylint: disable=line-too-long\n \"\"\"Checks the validity of the version of the give CWL document.\n \n Returns the document and the validated version string.\n \"\"\"\n if isinstance(doc, list):\n metadata = metadata.copy()\n- metadata[\"$graph\"] = doc\n+ metadata[u\"$graph\"] = doc\n cdoc = metadata\n else:\n cdoc = doc\n \n- version = cdoc[\"cwlVersion\"]\n+ version = cdoc[u\"cwlVersion\"]\n \n if version not in UPDATES:\n if version in DEVUPDATES:\n@@ -398,16 +418,16 @@ def checkversion(doc, metadata, enable_dev):\n return (cdoc, version)\n \n def update(doc, loader, baseuri, enable_dev, metadata):\n- # type: (Any, Loader, str, bool, Any) -> Any\n+ # type: (Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader, str, bool, Any) -> Dict[unicode, Any]\n \n- (doc, version) = checkversion(doc, metadata, enable_dev)\n+ (cdoc, version) = checkversion(doc, metadata, enable_dev)\n \n- nextupdate = identity\n+ nextupdate = identity # type: Callable[[Any, Loader, str], Tuple[Any, str]]\n \n while nextupdate:\n- (doc, version) = nextupdate(doc, loader, baseuri)\n+ (cdoc, version) = nextupdate(cdoc, loader, baseuri)\n nextupdate = ALLUPDATES[version]\n \n- doc[\"cwlVersion\"] = version\n+ cdoc[u\"cwlVersion\"] = version\n \n- return doc\n+ return cdoc\ndiff --git a/cwltool/workflow.py b/cwltool/workflow.py\n--- a/cwltool/workflow.py\n+++ b/cwltool/workflow.py\n@@ -54,7 +54,7 @@ def findfiles(wo, fn=None): # type: (Any, List) -> List[Dict[str, Any]]\n \n \n def match_types(sinktype, src, iid, inputobj, linkMerge, valueFrom):\n- # type: (Union[List[str],str], WorkflowStateItem, str, Dict[str, Any], str, str) -> bool\n+ # type: (Union[List[str],str], WorkflowStateItem, str, Dict[unicode, Any], str, str) -> bool\n if isinstance(sinktype, list):\n # Sink is union type\n for st in sinktype:\n@@ -104,25 +104,37 @@ def are_same_type(src, sink): # type: (Any, Any) -> bool\n return src == sink\n \n \n-def object_from_state(state, parms, frag_only, supportsMultipleInput):\n- # type: (Dict[str,WorkflowStateItem], List[Dict[str, Any]], bool, bool) -> Dict[str, str]\n- inputobj = {} # type: Dict[str, str]\n+def object_from_state(state, parms, frag_only, supportsMultipleInput, sourceField):\n+ # type: (Dict[unicode, WorkflowStateItem], List[Dict[unicode, Any]], bool, bool, unicode) -> Dict[unicode, Any]\n+ inputobj = {} # type: Dict[unicode, Any]\n for inp in parms:\n iid = inp[\"id\"]\n if frag_only:\n iid = shortname(iid)\n- if \"source\" in inp:\n- if isinstance(inp[\"source\"], list) and not supportsMultipleInput:\n- raise WorkflowException(\"Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\")\n- connections = aslist(inp[\"source\"])\n+ if sourceField in inp:\n+ if (isinstance(inp[sourceField], list) and not\n+ supportsMultipleInput):\n+ raise WorkflowException(\n+ \"Workflow contains multiple inbound links to a single \"\n+ \"parameter but MultipleInputFeatureRequirement is not \"\n+ \"declared.\")\n+ connections = aslist(inp[sourceField])\n for src in connections:\n if src in state and state[src] is not None:\n- if not match_types(inp[\"type\"], state[src], iid, inputobj,\n- inp.get(\"linkMerge\", (\"merge_nested\" if len(connections) > 1 else None)),\n- valueFrom=inp.get(\"valueFrom\")):\n- raise WorkflowException(u\"Type mismatch between source '%s' (%s) and sink '%s' (%s)\" % (src, state[src].parameter[\"type\"], inp[\"id\"], inp[\"type\"]))\n+ if not match_types(\n+ inp[\"type\"], state[src], iid, inputobj,\n+ inp.get(\"linkMerge\", (\"merge_nested\"\n+ if len(connections) > 1 else None)),\n+ valueFrom=inp.get(\"valueFrom\")):\n+ raise WorkflowException(\n+ u\"Type mismatch between source '%s' (%s) and \"\n+ \"sink '%s' (%s)\" % (src,\n+ state[src].parameter[\"type\"], inp[\"id\"],\n+ inp[\"type\"]))\n elif src not in state:\n- raise WorkflowException(u\"Connect source '%s' on parameter '%s' does not exist\" % (src, inp[\"id\"]))\n+ raise WorkflowException(\n+ u\"Connect source '%s' on parameter '%s' does not \"\n+ \"exist\" % (src, inp[\"id\"]))\n else:\n return None\n elif \"default\" in inp:\n@@ -146,7 +158,7 @@ def __init__(self, step): # type: (Any) -> None\n self.name = uniquename(u\"step %s\" % shortname(self.id))\n \n def job(self, joborder, output_callback, **kwargs):\n- # type: (Dict[str,str], str, functools.partial[None], **Any) -> Generator\n+ # type: (Dict[unicode, unicode], functools.partial[None], **Any) -> Generator\n kwargs[\"part_of\"] = self.name\n kwargs[\"name\"] = shortname(self.id)\n for j in self.step.job(joborder, output_callback, **kwargs):\n@@ -161,7 +173,7 @@ def __init__(self, workflow, **kwargs):\n self.tool = workflow.tool\n self.steps = [WorkflowJobStep(s) for s in workflow.steps]\n self.id = workflow.tool[\"id\"]\n- self.state = None # type: Dict[str, WorkflowStateItem]\n+ self.state = None # type: Dict[unicode, WorkflowStateItem]\n self.processStatus = None # type: str\n if \"outdir\" in kwargs:\n self.outdir = kwargs[\"outdir\"]\n@@ -198,14 +210,17 @@ def receive_output(self, step, outputparms, jobout, processStatus):\n step.completed = True\n \n def try_make_job(self, step, **kwargs):\n- # type: (WorkflowJobStep, str, **Any) -> Generator\n+ # type: (WorkflowJobStep, **Any) -> Generator\n inputparms = step.tool[\"inputs\"]\n outputparms = step.tool[\"outputs\"]\n \n- supportsMultipleInput = bool(self.workflow.get_requirement(\"MultipleInputFeatureRequirement\")[0])\n+ supportsMultipleInput = bool(self.workflow.get_requirement(\n+ \"MultipleInputFeatureRequirement\")[0])\n \n try:\n- inputobj = object_from_state(self.state, inputparms, False, supportsMultipleInput)\n+ inputobj = object_from_state(\n+ self.state, inputparms, False, supportsMultipleInput,\n+ \"source\")\n if inputobj is None:\n _logger.debug(u\"[%s] job step %s not ready\", self.name, step.id)\n return\n@@ -217,7 +232,9 @@ def try_make_job(self, step, **kwargs):\n \n callback = functools.partial(self.receive_output, step, outputparms)\n \n- valueFrom = {i[\"id\"]: i[\"valueFrom\"] for i in step.tool[\"inputs\"] if \"valueFrom\" in i}\n+ valueFrom = {\n+ i[\"id\"]: i[\"valueFrom\"] for i in step.tool[\"inputs\"]\n+ if \"valueFrom\" in i}\n \n if len(valueFrom) > 0 and not bool(self.workflow.get_requirement(\"StepInputExpressionRequirement\")[0]):\n raise WorkflowException(\"Workflow step contains valueFrom but StepInputExpressionRequirement not in requirements\")\n@@ -225,8 +242,9 @@ def try_make_job(self, step, **kwargs):\n vfinputs = {shortname(k): v for k,v in inputobj.iteritems()}\n def valueFromFunc(k, v): # type: (Any, Any) -> Any\n if k in valueFrom:\n- return expression.do_eval(valueFrom[k], vfinputs, self.workflow.requirements,\n- None, None, {}, context=v)\n+ return expression.do_eval(\n+ valueFrom[k], vfinputs, self.workflow.requirements,\n+ None, None, {}, context=v)\n else:\n return v\n \n@@ -279,7 +297,7 @@ def run(self, **kwargs):\n _logger.debug(u\"[%s] workflow starting\", self.name)\n \n def job(self, joborder, output_callback, move_outputs=True, **kwargs):\n- # type: (Dict[str,str], str, Callable[[Any, Any], Any], bool, **Any) -> Generator[WorkflowJob, None, None]\n+ # type: (Dict[unicode, Any], Callable[[Any, Any], Any], bool, **Any) -> Generator[WorkflowJob, None, None]\n self.state = {}\n self.processStatus = \"success\"\n \n@@ -326,7 +344,7 @@ def job(self, joborder, output_callback, move_outputs=True, **kwargs):\n \n supportsMultipleInput = bool(self.workflow.get_requirement(\"MultipleInputFeatureRequirement\")[0])\n \n- wo = object_from_state(self.state, self.tool[\"outputs\"], True, supportsMultipleInput)\n+ wo = object_from_state(self.state, self.tool[\"outputs\"], True, supportsMultipleInput, \"outputSource\")\n \n if wo is None:\n raise WorkflowException(\"Output for workflow not available\")\n@@ -375,7 +393,7 @@ def job(self, joborder, output_callback, move_outputs=True, **kwargs):\n \n class Workflow(Process):\n def __init__(self, toolpath_object, **kwargs):\n- # type: (Dict[str, Any], **Any) -> None\n+ # type: (Dict[unicode, Any], **Any) -> None\n super(Workflow, self).__init__(toolpath_object, **kwargs)\n \n kwargs[\"requirements\"] = self.requirements\n@@ -388,7 +406,7 @@ def __init__(self, toolpath_object, **kwargs):\n # TODO: statically validate data links instead of doing it at runtime.\n \n def job(self, joborder, output_callback, **kwargs):\n- # type: (Dict[str,str], str, Callable[[Any, Any], Any], **Any) -> Generator[WorkflowJob, None, None]\n+ # type: (Dict[unicode, unicode], Callable[[Any, Any], Any], **Any) -> Generator[WorkflowJob, None, None]\n builder = self._init_job(joborder, **kwargs)\n wj = WorkflowJob(self, **kwargs)\n yield wj\n@@ -407,7 +425,7 @@ def visit(self, op):\n class WorkflowStep(Process):\n \n def __init__(self, toolpath_object, pos, **kwargs):\n- # type: (Dict[str, Any], int, **Any) -> None\n+ # type: (Dict[unicode, Any], int, **Any) -> None\n if \"id\" in toolpath_object:\n self.id = toolpath_object[\"id\"]\n else:\n@@ -486,7 +504,7 @@ def __init__(self, toolpath_object, pos, **kwargs):\n self.tool[\"outputs\"] = outputparms\n \n def receive_output(self, output_callback, jobout, processStatus):\n- # type: (Callable[...,Any], Dict[str, str], str) -> None\n+ # type: (Callable[...,Any], Dict[unicode, str], str) -> None\n #_logger.debug(\"WorkflowStep output from run is %s\", jobout)\n output = {}\n for i in self.tool[\"outputs\"]:\n@@ -498,7 +516,7 @@ def receive_output(self, output_callback, jobout, processStatus):\n output_callback(output, processStatus)\n \n def job(self, joborder, output_callback, **kwargs):\n- # type: (Dict[str, Any], str, Callable[...,Any], **Any) -> Generator\n+ # type: (Dict[unicode, Any], Callable[...,Any], **Any) -> Generator\n for i in self.tool[\"inputs\"]:\n p = i[\"id\"]\n field = shortname(p)\n@@ -555,7 +573,7 @@ def setTotal(self, total): # type: (int) -> None\n \n \n def dotproduct_scatter(process, joborder, scatter_keys, output_callback, **kwargs):\n- # type: (WorkflowJobStep, Dict[str, Any], str, List[str], Callable[..., Any], **Any) -> Generator[WorkflowJob, None, None]\n+ # type: (WorkflowJobStep, Dict[unicode, Any], List[str], Callable[..., Any], **Any) -> Generator[WorkflowJob, None, None]\n l = None\n for s in scatter_keys:\n if l is None:\n@@ -581,7 +599,7 @@ def dotproduct_scatter(process, joborder, scatter_keys, output_callback, **kwarg\n \n \n def nested_crossproduct_scatter(process, joborder, scatter_keys, output_callback, **kwargs):\n- # type: (WorkflowJobStep, Dict[str, Any], str, List[str], Callable[..., Any], **Any) -> Generator[WorkflowJob, None, None]\n+ # type: (WorkflowJobStep, Dict[unicode, Any], List[str], Callable[..., Any], **Any) -> Generator[WorkflowJob, None, None]\n scatter_key = scatter_keys[0]\n l = len(joborder[scatter_key])\n output = {} # type: Dict[str,List[str]]\n@@ -610,7 +628,7 @@ def nested_crossproduct_scatter(process, joborder, scatter_keys, output_callback\n \n \n def crossproduct_size(joborder, scatter_keys):\n- # type: (Dict[str, Any], List[str]) -> int\n+ # type: (Dict[unicode, Any], List[str]) -> int\n scatter_key = scatter_keys[0]\n if len(scatter_keys) == 1:\n sum = len(joborder[scatter_key])\n@@ -623,7 +641,7 @@ def crossproduct_size(joborder, scatter_keys):\n return sum\n \n def flat_crossproduct_scatter(process, joborder, scatter_keys, output_callback, startindex, **kwargs):\n- # type: (WorkflowJobStep, Dict[str, Any], str, List[str], Union[ReceiveScatterOutput,Callable[..., Any]], int, **Any) -> Generator[WorkflowJob, None, None]\n+ # type: (WorkflowJobStep, Dict[unicode, Any], List[str], Union[ReceiveScatterOutput,Callable[..., Any]], int, **Any) -> Generator[WorkflowJob, None, None]\n scatter_key = scatter_keys[0]\n l = len(joborder[scatter_key])\n rc = None # type: ReceiveScatterOutput\ndiff --git a/setup.py b/setup.py\n--- a/setup.py\n+++ b/setup.py\n@@ -41,7 +41,7 @@\n 'rdflib >= 4.1.0',\n 'rdflib-jsonld >= 0.3.0',\n 'shellescape',\n- 'schema-salad==1.11.20160524152859',\n+ 'schema-salad==1.12.20160610104117',\n 'typing'\n ],\n test_suite='tests',\n", "test_patch": "diff --git a/cwltool/schemas/draft-4/salad/tests/Process.yml b/cwltool/schemas/draft-4/salad/tests/Process.yml\nnew file mode 100644\n--- /dev/null\n+++ b/cwltool/schemas/draft-4/salad/tests/Process.yml\n@@ -0,0 +1,36 @@\n+$base: \"https://w3id.org/cwl/cwl#\"\n+\n+$namespaces:\n+ cwl: \"https://w3id.org/cwl/cwl#\"\n+ sld: \"https://w3id.org/cwl/salad#\"\n+\n+$graph:\n+\n+- $import: \"../schema_salad/metaschema/metaschema_base.yml\"\n+\n+- name: InputBinding\n+ type: record\n+ abstract: true\n+ fields:\n+ - name: loadContents\n+ type:\n+ - \"null\"\n+ - boolean\n+ jsonldPredicate: \"cwl:loadContents\"\n+ doc: |\n+ Only valid when `type: File` or is an array of `items: File`.\n+\n+ Read up to the first 64 KiB of text from the file and place it in the\n+ \"contents\" field of the file object for use by expressions.\n+\n+- name: InputRecordField\n+ type: record\n+ extends: \"sld:RecordField\"\n+ fields:\n+ - name: inputBinding\n+ type: [ \"null\", \"#InputBinding\" ]\n+ jsonldPredicate: \"cwl:inputBinding\"\n+\n+- name: Blurb\n+ type: record\n+ extends: InputBinding\n\\ No newline at end of file\ndiff --git a/cwltool/schemas/draft-4/salad/tests/test_examples.py b/cwltool/schemas/draft-4/salad/tests/test_examples.py\n--- a/cwltool/schemas/draft-4/salad/tests/test_examples.py\n+++ b/cwltool/schemas/draft-4/salad/tests/test_examples.py\n@@ -3,25 +3,28 @@\n import schema_salad.main\n import schema_salad.schema\n import rdflib\n-import yaml\n+import ruamel.yaml as yaml\n+try:\n+ from ruamel.yaml import CSafeLoader as SafeLoader\n+except ImportError:\n+ from ruamel.yaml import SafeLoader\n+\n \n class TestSchemas(unittest.TestCase):\n def test_schemas(self):\n l = schema_salad.ref_resolver.Loader({})\n \n ra, _ = l.resolve_all({\n- \"$schemas\": [\"tests/EDAM.owl\"],\n- \"$namespaces\": {\"edam\": \"http://edamontology.org/\"},\n- \"edam:has_format\": \"edam:format_1915\"\n- }, \"\")\n-\n- self.assertEqual(ra, {\n- \"$schemas\": [\"tests/EDAM.owl\"],\n- \"$namespaces\": {\"edam\": \"http://edamontology.org/\"},\n- 'http://edamontology.org/has_format': 'http://edamontology.org/format_1915'\n- })\n-\n+ u\"$schemas\": [u\"tests/EDAM.owl\"],\n+ u\"$namespaces\": {u\"edam\": u\"http://edamontology.org/\"},\n+ u\"edam:has_format\": u\"edam:format_1915\"\n+ }, \"\")\n \n+ self.assertEqual({\n+ u\"$schemas\": [u\"tests/EDAM.owl\"],\n+ u\"$namespaces\": {u\"edam\": u\"http://edamontology.org/\"},\n+ u'http://edamontology.org/has_format': u'http://edamontology.org/format_1915'\n+ }, ra)\n \n # def test_domain(self):\n # l = schema_salad.ref_resolver.Loader({})\n@@ -43,12 +46,15 @@ def test_schemas(self):\n # })\n \n def test_self_validate(self):\n- schema_salad.main.main(args=[\"schema_salad/metaschema/metaschema.yml\"])\n- schema_salad.main.main(args=[\"schema_salad/metaschema/metaschema.yml\",\n- \"schema_salad/metaschema/metaschema.yml\"])\n+ self.assertEqual(0, schema_salad.main.main(argsl=[\"schema_salad/metaschema/metaschema.yml\"]))\n+ self.assertEqual(0, schema_salad.main.main(argsl=[\"schema_salad/metaschema/metaschema.yml\",\n+ \"schema_salad/metaschema/metaschema.yml\"]))\n+\n+ def test_avro_regression(self):\n+ self.assertEqual(0, schema_salad.main.main(argsl=[\"tests/Process.yml\"]))\n \n def test_jsonld_ctx(self):\n- ldr, _, _ = schema_salad.schema.load_schema({\n+ ldr, _, _, _ = schema_salad.schema.load_schema({\n \"$base\": \"Y\",\n \"name\": \"X\",\n \"$namespaces\": {\n@@ -80,7 +86,7 @@ def test_idmap(self):\n \"@type\": \"@id\",\n \"identity\": True,\n },\n- \"id\": \"@id\"})\n+ \"id\": \"@id\"})\n \n ra, _ = ldr.resolve_all({\n \"id\": \"stuff\",\n@@ -94,28 +100,154 @@ def test_idmap(self):\n }\n }, \"http://example2.com/\")\n \n- self.assertEqual(ra,\n- {\n- \"id\": \"http://example2.com/#stuff\",\n- 'inputs': [{'a': 2, 'id': 'http://example2.com/#stuff/zing'},\n- {'a': 1, 'id': 'http://example2.com/#stuff/zip'}],\n- 'outputs': ['http://example2.com/#stuff/out'],\n- 'other': {\n- 'n': 9\n- }\n- }\n- )\n+ self.assertEqual(\"http://example2.com/#stuff\", ra[\"id\"])\n+ for item in ra[\"inputs\"]:\n+ if item[\"a\"] == 2:\n+ self.assertEquals('http://example2.com/#stuff/zing', item[\"id\"])\n+ else:\n+ self.assertEquals('http://example2.com/#stuff/zip', item[\"id\"])\n+ self.assertEquals(['http://example2.com/#stuff/out'], ra['outputs'])\n+ self.assertEquals({'n': 9}, ra['other'])\n+\n+ def test_scoped_ref(self):\n+ ldr = schema_salad.ref_resolver.Loader({})\n+ ldr.add_context({\n+ \"scatter\": {\n+ \"@type\": \"@id\",\n+ \"refScope\": 0,\n+ },\n+ \"source\": {\n+ \"@type\": \"@id\",\n+ \"refScope\": 2,\n+ },\n+ \"in\": {\n+ \"mapSubject\": \"id\",\n+ \"mapPredicate\": \"source\"\n+ },\n+ \"out\": {\n+ \"@type\": \"@id\",\n+ \"identity\": True\n+ },\n+ \"inputs\": {\n+ \"mapSubject\": \"id\",\n+ \"mapPredicate\": \"type\"\n+ },\n+ \"outputs\": {\n+ \"mapSubject\": \"id\",\n+ },\n+ \"steps\": {\n+ \"mapSubject\": \"id\"\n+ },\n+ \"id\": \"@id\"})\n+\n+ ra, _ = ldr.resolve_all({\n+ \"inputs\": {\n+ \"inp\": \"string\",\n+ \"inp2\": \"string\"\n+ },\n+ \"outputs\": {\n+ \"out\": {\n+ \"type\": \"string\",\n+ \"source\": \"step2/out\"\n+ }\n+ },\n+ \"steps\": {\n+ \"step1\": {\n+ \"in\": {\n+ \"inp\": \"inp\",\n+ \"inp2\": \"#inp2\",\n+ \"inp3\": [\"inp\", \"inp2\"]\n+ },\n+ \"out\": [\"out\"],\n+ \"scatter\": \"inp\"\n+ },\n+ \"step2\": {\n+ \"in\": {\n+ \"inp\": \"step1/out\"\n+ },\n+ \"scatter\": \"inp\",\n+ \"out\": [\"out\"]\n+ }\n+ }\n+ }, \"http://example2.com/\")\n+\n+ self.assertEquals(\n+ {'inputs': [{\n+ 'id': 'http://example2.com/#inp',\n+ 'type': 'string'\n+ }, {\n+ 'id': 'http://example2.com/#inp2',\n+ 'type': 'string'\n+ }],\n+ 'outputs': [{\n+ 'id': 'http://example2.com/#out',\n+ 'type': 'string',\n+ 'source': 'http://example2.com/#step2/out'\n+ }],\n+ 'steps': [{\n+ 'id': 'http://example2.com/#step1',\n+ 'scatter': 'http://example2.com/#step1/inp',\n+ 'in': [{\n+ 'id': 'http://example2.com/#step1/inp',\n+ 'source': 'http://example2.com/#inp'\n+ }, {\n+ 'id': 'http://example2.com/#step1/inp2',\n+ 'source': 'http://example2.com/#inp2'\n+ }, {\n+ 'id': 'http://example2.com/#step1/inp3',\n+ 'source': ['http://example2.com/#inp', 'http://example2.com/#inp2']\n+ }],\n+ \"out\": [\"http://example2.com/#step1/out\"],\n+ }, {\n+ 'id': 'http://example2.com/#step2',\n+ 'scatter': 'http://example2.com/#step2/inp',\n+ 'in': [{\n+ 'id': 'http://example2.com/#step2/inp',\n+ 'source': 'http://example2.com/#step1/out'\n+ }],\n+ \"out\": [\"http://example2.com/#step2/out\"],\n+ }]\n+ }, ra)\n+\n \n def test_examples(self):\n self.maxDiff = None\n for a in [\"field_name\", \"ident_res\", \"link_res\", \"vocab_res\"]:\n- ldr, _, _ = schema_salad.schema.load_schema(\"schema_salad/metaschema/%s_schema.yml\" % a)\n+ ldr, _, _, _ = schema_salad.schema.load_schema(\n+ \"schema_salad/metaschema/%s_schema.yml\" % a)\n with open(\"schema_salad/metaschema/%s_src.yml\" % a) as src_fp:\n- src = ldr.resolve_all(yaml.load(src_fp), \"\")[0]\n+ src = ldr.resolve_all(\n+ yaml.load(src_fp, Loader=SafeLoader), \"\", checklinks=False)[0]\n with open(\"schema_salad/metaschema/%s_proc.yml\" % a) as src_proc:\n- proc = yaml.load(src_proc)\n+ proc = yaml.load(src_proc, Loader=SafeLoader)\n self.assertEqual(proc, src)\n \n+ def test_yaml_float_test(self):\n+ self.assertEqual(yaml.load(\"float-test: 2e-10\")[\"float-test\"], 2e-10)\n+\n+ def test_typedsl_ref(self):\n+ ldr = schema_salad.ref_resolver.Loader({})\n+ ldr.add_context({\n+ \"File\": \"http://example.com/File\",\n+ \"null\": \"http://example.com/null\",\n+ \"array\": \"http://example.com/array\",\n+ \"type\": {\n+ \"@type\": \"@vocab\",\n+ \"typeDSL\": True\n+ }\n+ })\n+\n+ ra, _ = ldr.resolve_all({\"type\": \"File\"}, \"\")\n+ self.assertEqual({'type': 'File'}, ra)\n+\n+ ra, _ = ldr.resolve_all({\"type\": \"File?\"}, \"\")\n+ self.assertEqual({'type': ['null', 'File']}, ra)\n+\n+ ra, _ = ldr.resolve_all({\"type\": \"File[]\"}, \"\")\n+ self.assertEqual({'type': {'items': 'File', 'type': 'array'}}, ra)\n+\n+ ra, _ = ldr.resolve_all({\"type\": \"File[]?\"}, \"\")\n+ self.assertEqual({'type': ['null', {'items': 'File', 'type': 'array'}]}, ra)\n \n if __name__ == '__main__':\n unittest.main()\n", "problem_statement": "", "hints_text": "", "created_at": "2016-06-08T13:17:05Z"}
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