Merge pull request #589 from common-workflow-language/faster_parse

mr-c · web-flow · commit f691bf1aa66f · 2017-12-27T23:20:58.000+02:00
reduce loading time for packed documents
diff --git a/cwltool/load_tool.py b/cwltool/load_tool.py
@@ -1,6 +1,6 @@
+"""Loads a CWL document."""
 from __future__ import absolute_import
 # pylint: disable=unused-import
-"""Loads a CWL document."""
 
 import logging
 import os
@@ -9,34 +9,34 @@
 import hashlib
 import json
 import copy
-from typing import Any, Callable, Dict, List, Text, Tuple, Union, cast, Iterable
+from typing import (Any, Callable, Dict, Iterable, List, Mapping, Optional,
+        Text, Tuple, Union, cast)
 
 import requests.sessions
 from six import itervalues, string_types
+from six.moves import urllib
 
 import schema_salad.schema as schema
 from avro.schema import Names
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
-from schema_salad.ref_resolver import Fetcher, Loader, file_uri
+from schema_salad.ref_resolver import ContextType, Fetcher, Loader, file_uri
 from schema_salad.sourceline import cmap
 from schema_salad.validate import ValidationException
-from six.moves import urllib
 
 from . import process, update
 from .errors import WorkflowException
 from .process import Process, shortname, get_schema
 from .update import ALLUPDATES
 
 _logger = logging.getLogger("cwltool")
-
 jobloaderctx = {
     u"cwl": "https://w3id.org/cwl/cwl#",
     u"cwltool": "http://commonwl.org/cwltool#",
     u"path": {u"@type": u"@id"},
     u"location": {u"@type": u"@id"},
     u"format": {u"@type": u"@id"},
     u"id": u"@id"
-}
+}  # type: ContextType
 
 
 overrides_ctx = {
@@ -51,26 +51,39 @@
         "@id": "cwltool:override",
         "mapSubject": "class"
     }
-}  # type: Dict[Text, Union[Dict[Any, Any], Text, Iterable[Text]]]
+}  # type: ContextType
+
+
+FetcherConstructorType = Callable[[Dict[Text, Union[Text, bool]],
+    requests.sessions.Session], Fetcher]
+
+loaders = {}  # type: Dict[FetcherConstructorType, Loader]
+
+def default_loader(fetcher_constructor):
+    # type: (Optional[FetcherConstructorType]) -> Loader
+    if fetcher_constructor in loaders:
+        return loaders[fetcher_constructor]
+    else:
+        loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)
+        loaders[fetcher_constructor] = loader
+        return loader
 
 def resolve_tool_uri(argsworkflow,  # type: Text
                      resolver=None,  # type: Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
-                     fetcher_constructor=None,
-                     # type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
+                     fetcher_constructor=None,  # type: FetcherConstructorType
                      document_loader=None  # type: Loader
-):
-    # type: (...) -> Tuple[Text, Text]
+                     ):  # type: (...) -> Tuple[Text, Text]
 
     uri = None  # type: Text
     split = urllib.parse.urlsplit(argsworkflow)
     # In case of Windows path, urlsplit misjudge Drive letters as scheme, here we are skipping that
-    if split.scheme and split.scheme in [u'http',u'https',u'file']:
+    if split.scheme and split.scheme in [u'http', u'https', u'file']:
         uri = argsworkflow
     elif os.path.exists(os.path.abspath(argsworkflow)):
         uri = file_uri(str(os.path.abspath(argsworkflow)))
     elif resolver:
         if document_loader is None:
-            document_loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)  # type: ignore
+            document_loader = default_loader(fetcher_constructor)  # type: ignore
         uri = resolver(document_loader, argsworkflow)
 
     if uri is None:
@@ -85,18 +98,17 @@ def resolve_tool_uri(argsworkflow,  # type: Text
 
 def fetch_document(argsworkflow,  # type: Union[Text, Dict[Text, Any]]
                    resolver=None,  # type: Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
-                   fetcher_constructor=None
-                   # type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
-                   ):
-    # type: (...) -> Tuple[Loader, CommentedMap, Text]
+                   fetcher_constructor=None  # type: FetcherConstructorType
+                  ):  # type: (...) -> Tuple[Loader, CommentedMap, Text]
     """Retrieve a CWL document."""
 
-    document_loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)  # type: ignore
+    document_loader = default_loader(fetcher_constructor)  # type: ignore
 
     uri = None  # type: Text
     workflowobj = None  # type: CommentedMap
     if isinstance(argsworkflow, string_types):
-        uri, fileuri = resolve_tool_uri(argsworkflow, resolver=resolver, document_loader=document_loader)
+        uri, fileuri = resolve_tool_uri(argsworkflow, resolver=resolver,
+                document_loader=document_loader)
         workflowobj = document_loader.fetch(fileuri)
     elif isinstance(argsworkflow, dict):
         uri = "#" + Text(id(argsworkflow))
@@ -126,7 +138,7 @@ def _convert_stdstreams_to_files(workflowobj):
                                         sort_keys=True).encode('utf-8')).hexdigest())
                             workflowobj[streamtype] = filename
                         out['type'] = 'File'
-                        out['outputBinding'] = {'glob': filename}
+                        out['outputBinding'] = cmap({'glob': filename})
             for inp in workflowobj.get('inputs', []):
                 if inp.get('type') == 'stdin':
                     if 'inputBinding' in inp:
@@ -170,25 +182,25 @@ def validate_document(document_loader,  # type: Loader
                       enable_dev=False,  # type: bool
                       strict=True,  # type: bool
                       preprocess_only=False,  # type: bool
-                      fetcher_constructor=None,
-                      skip_schemas=None,
-                      # type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
-                      overrides=None  # type: List[Dict]
+                      fetcher_constructor=None,  # type: FetcherConstructorType
+                      skip_schemas=None,  # type: bool
+                      overrides=None,  # type: List[Dict]
+                      metadata=None,  # type: Optional[Dict]
                       ):
     # type: (...) -> Tuple[Loader, Names, Union[Dict[Text, Any], List[Dict[Text, Any]]], Dict[Text, Any], Text]
     """Validate a CWL document."""
 
     if isinstance(workflowobj, list):
-        workflowobj = {
+        workflowobj = cmap({
             "$graph": workflowobj
-        }
+        }, fn=uri)
 
     if not isinstance(workflowobj, dict):
         raise ValueError("workflowjobj must be a dict, got '%s': %s" % (type(workflowobj), workflowobj))
 
     jobobj = None
     if "cwl:tool" in workflowobj:
-        job_loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)  # type: ignore
+        job_loader = default_loader(fetcher_constructor)  # type: ignore
         jobobj, _ = job_loader.resolve_all(workflowobj, uri)
         uri = urllib.parse.urljoin(uri, workflowobj["https://w3id.org/cwl/cwl#tool"])
         del cast(dict, jobobj)["https://w3id.org/cwl/cwl#tool"]
@@ -200,22 +212,25 @@ def validate_document(document_loader,  # type: Loader
         workflowobj = fetch_document(uri, fetcher_constructor=fetcher_constructor)[1]
 
     fileuri = urllib.parse.urldefrag(uri)[0]
-
-    if "cwlVersion" in workflowobj:
-        if not isinstance(workflowobj["cwlVersion"], (str, Text)):
-            raise Exception("'cwlVersion' must be a string, got %s" % type(workflowobj["cwlVersion"]))
-        # strip out version
-        workflowobj["cwlVersion"] = re.sub(
-            r"^(?:cwl:|https://w3id.org/cwl/cwl#)", "",
-            workflowobj["cwlVersion"])
-        if workflowobj["cwlVersion"] not in list(ALLUPDATES):
-            # print out all the Supported Versions of cwlVersion
-            versions = list(ALLUPDATES) # ALLUPDATES is a dict
-            versions.sort()
-            raise ValidationException("'cwlVersion' not valid. Supported CWL versions are: \n{}".format("\n".join(versions)))
-    else:
-        raise ValidationException("No cwlVersion found."
-            "Use the following syntax in your CWL workflow to declare version: cwlVersion: <version>")
+    if "cwlVersion" not in workflowobj:
+        if metadata and 'cwlVersion' in metadata:
+            workflowobj['cwlVersion'] = metadata['cwlVersion']
+        else:
+            raise ValidationException("No cwlVersion found."
+                "Use the following syntax in your CWL document to declare "
+                "the version: cwlVersion: <version>")
+
+    if not isinstance(workflowobj["cwlVersion"], (str, Text)):
+        raise Exception("'cwlVersion' must be a string, got %s" % type(workflowobj["cwlVersion"]))
+    # strip out version
+    workflowobj["cwlVersion"] = re.sub(
+        r"^(?:cwl:|https://w3id.org/cwl/cwl#)", "",
+        workflowobj["cwlVersion"])
+    if workflowobj["cwlVersion"] not in list(ALLUPDATES):
+        # print out all the Supported Versions of cwlVersion
+        versions = list(ALLUPDATES)  # ALLUPDATES is a dict
+        versions.sort()
+        raise ValidationException("'cwlVersion' not valid. Supported CWL versions are: \n{}".format("\n".join(versions)))
 
     if workflowobj["cwlVersion"] == "draft-2":
         workflowobj = cast(CommentedMap, cmap(update._draft2toDraft3dev1(
@@ -238,36 +253,36 @@ def validate_document(document_loader,  # type: Loader
     _add_blank_ids(workflowobj)
 
     workflowobj["id"] = fileuri
-    processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)
+    processobj, new_metadata = document_loader.resolve_all(workflowobj, fileuri)
     if not isinstance(processobj, (CommentedMap, CommentedSeq)):
         raise ValidationException("Workflow must be a dict or list.")
 
-    if not metadata:
+    if not new_metadata:
         if not isinstance(processobj, dict):
             raise ValidationException("Draft-2 workflows must be a dict.")
-        metadata = cast(CommentedMap, cmap({"$namespaces": processobj.get("$namespaces", {}),
-                                            "$schemas": processobj.get("$schemas", []),
-                                            "cwlVersion": processobj["cwlVersion"]},
-                                           fn=fileuri))
+        new_metadata = cast(CommentedMap, cmap(
+            {"$namespaces": processobj.get("$namespaces", {}),
+             "$schemas": processobj.get("$schemas", []),
+             "cwlVersion": processobj["cwlVersion"]}, fn=fileuri))
 
     _convert_stdstreams_to_files(workflowobj)
 
     if preprocess_only:
-        return document_loader, avsc_names, processobj, metadata, uri
+        return document_loader, avsc_names, processobj, new_metadata, uri
 
     schema.validate_doc(avsc_names, processobj, document_loader, strict)
 
-    if metadata.get("cwlVersion") != update.LATEST:
+    if new_metadata.get("cwlVersion") != update.LATEST:
         processobj = cast(CommentedMap, cmap(update.update(
-            processobj, document_loader, fileuri, enable_dev, metadata)))
+            processobj, document_loader, fileuri, enable_dev, new_metadata)))
 
     if jobobj:
-        metadata[u"cwl:defaults"] = jobobj
+        new_metadata[u"cwl:defaults"] = jobobj
 
     if overrides:
-        metadata[u"cwltool:overrides"] = overrides
+        new_metadata[u"cwltool:overrides"] = overrides
 
-    return document_loader, avsc_names, processobj, metadata, uri
+    return document_loader, avsc_names, processobj, new_metadata, uri
 
 
 def make_tool(document_loader,  # type: Loader
@@ -322,7 +337,7 @@ def load_tool(argsworkflow,  # type: Union[Text, Dict[Text, Any]]
               enable_dev=False,  # type: bool
               strict=True,  # type: bool
               resolver=None,  # type: Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
-              fetcher_constructor=None,  # type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
+              fetcher_constructor=None,  # type: FetcherConstructorType
               overrides=None
               ):
     # type: (...) -> Process
@@ -332,7 +347,8 @@ def load_tool(argsworkflow,  # type: Union[Text, Dict[Text, Any]]
     document_loader, avsc_names, processobj, metadata, uri = validate_document(
         document_loader, workflowobj, uri, enable_dev=enable_dev,
         strict=strict, fetcher_constructor=fetcher_constructor,
-        overrides=overrides)
+        overrides=overrides, metadata=kwargs.get('metadata', None)
+        if kwargs else None)
     return make_tool(document_loader, avsc_names, metadata, uri,
                      makeTool, kwargs if kwargs else {})
 
diff --git a/cwltool/main.py b/cwltool/main.py
@@ -27,8 +27,9 @@
 from .builder import Builder
 from .cwlrdf import printdot, printrdf
 from .errors import UnsupportedRequirement, WorkflowException
-from .load_tool import (resolve_tool_uri, fetch_document, make_tool, validate_document,
-                        jobloaderctx, resolve_overrides, load_overrides)
+from .load_tool import (FetcherConstructorType, resolve_tool_uri,
+        fetch_document, make_tool, validate_document, jobloaderctx,
+        resolve_overrides, load_overrides)
 from .mutation import MutationManager
 from .pack import pack
 from .pathmapper import (adjustDirObjs, adjustFileObjs, get_listing,
@@ -544,8 +545,8 @@ def load_job_order(args,   # type: argparse.Namespace
         job_order_object, _ = loader.resolve_ref(job_order_file, checklinks=False)
 
     if job_order_object and "http://commonwl.org/cwltool#overrides" in job_order_object:
-       overrides.extend(resolve_overrides(job_order_object, file_uri(job_order_file), tool_file_uri))
-       del job_order_object["http://commonwl.org/cwltool#overrides"]
+        overrides.extend(resolve_overrides(job_order_object, file_uri(job_order_file), tool_file_uri))
+        del job_order_object["http://commonwl.org/cwltool#overrides"]
 
     if not job_order_object:
         input_basedir = args.basedir if args.basedir else os.getcwd()
@@ -641,6 +642,7 @@ def addSizes(p):
     ns = {}  # type: Dict[Text, Union[Dict[Any, Any], Text, Iterable[Text]]]
     ns.update(t.metadata.get("$namespaces", {}))
     ld = Loader(ns)
+
     def expand_formats(p):
         if "format" in p:
             p["format"] = ld.expand_url(p["format"], "")
@@ -734,7 +736,7 @@ def main(argsl=None,  # type: List[str]
          versionfunc=versionstring,  # type: Callable[[], Text]
          job_order_object=None,  # type: MutableMapping[Text, Any]
          make_fs_access=StdFsAccess,  # type: Callable[[Text], StdFsAccess]
-         fetcher_constructor=None,  # type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
+         fetcher_constructor=None,  # type: FetcherConstructorType
          resolver=tool_resolver,
          logger_handler=None,
          custom_schema_callback=None  # type: Callable[[], None]
diff --git a/cwltool/workflow.py b/cwltool/workflow.py
@@ -70,11 +70,15 @@ def match_types(sinktype, src, iid, inputobj, linkMerge, valueFrom):
     elif isinstance(src.parameter["type"], list):
         # Source is union type
         # Check that at least one source type is compatible with the sink.
-        for st in src.parameter["type"]:
-            srccopy = copy.deepcopy(src)
-            srccopy.parameter["type"] = st
-            if match_types(sinktype, srccopy, iid, inputobj, linkMerge, valueFrom):
+        original_types = src.parameter["type"]
+        for source_type in original_types:
+            src.parameter["type"] = source_type
+            match = match_types(
+                sinktype, src, iid, inputobj, linkMerge, valueFrom)
+            if match:
+                src.parameter["type"] = original_types
                 return True
+        src.parameter["type"] = original_types
         return False
     elif linkMerge:
         if iid not in inputobj:
diff --git a/tests/test_pack.py b/tests/test_pack.py
@@ -12,6 +12,8 @@
 
 import cwltool.pack
 import cwltool.workflow
+from cwltool.resolver import tool_resolver
+from cwltool import load_tool
 from cwltool.load_tool import fetch_document, validate_document
 from cwltool.main import makeRelative, main, print_pack
 from cwltool.pathmapper import adjustDirObjs, adjustFileObjs
@@ -23,6 +25,7 @@ class TestPack(unittest.TestCase):
     maxDiff = None
 
     def test_pack(self):
+        load_tool.loaders = {}
 
         document_loader, workflowobj, uri = fetch_document(
             get_data("tests/wf/revsort.cwl"))
@@ -97,10 +100,11 @@ def _pack_idempotently(self, document):
                         reason="Instance of cwltool is used, on Windows it invokes a default docker container"
                                "which is not supported on AppVeyor")
     def test_packed_workflow_execution(self):
+        load_tool.loaders = {}
         test_wf = "tests/wf/count-lines1-wf.cwl"
         test_wf_job = "tests/wf/wc-job.json"
         document_loader, workflowobj, uri = fetch_document(
-            get_data(test_wf))
+            get_data(test_wf), resolver=tool_resolver)
         document_loader, avsc_names, processobj, metadata, uri = validate_document(
             document_loader, workflowobj, uri)
         packed = json.loads(print_pack(document_loader, processobj, uri, metadata))
