Merge branch 'patch-1' of https://github.com/mr-c/arvados into mr-c-patch-1

[arvados.git] / sdk / cwl / arvados_cwl / __init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 2b2acd5688ff3475c24af8242ae0a7c5ef3ffcd9..6f2255b3f8b18f104a00fc2d4982171c51dbb0da 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -16,43 +16,6 @@ import sys
 import re
 import pkg_resources  # part of setuptools
 
-### begin monkey patch ###
-# Monkey patch solution for bug #16169
-#
-# There is a bug in upstream cwltool where the version updater needs
-# to replace the document fragments in the loader index with the
-# updated ones, but actually it only does it for the root document.
-# Normally we just fix the bug in upstream but that's challenging
-# because current cwltool dropped support for Python 2.7 and we're
-# still supporting py2 in Arvados 2.0 (although py2 support will most
-# likely be dropped in Arvados 2.1).  Making a bugfix fork comes with
-# its own complications (it would need to be added to PyPi) so monkey
-# patching is the least disruptive fix (and is relatively safe because
-# our cwltool dependency is pinned to a specific version).  This
-# should be removed as soon as a bugfix goes into upstream cwltool and
-# we upgrade to it.
-#
-import cwltool.load_tool
-from cwltool.utils import visit_class
-from six.moves import urllib
-original_resolve_and_validate_document = cwltool.load_tool.resolve_and_validate_document
-def wrapped_resolve_and_validate_document(
-        loadingContext,            # type: LoadingContext
-        workflowobj,               # type: Union[CommentedMap, CommentedSeq]
-        uri,                       # type: Text
-        preprocess_only=False,     # type: bool
-        skip_schemas=None,         # type: Optional[bool]
-        ):
-    loadingContext, uri = original_resolve_and_validate_document(loadingContext, workflowobj, uri, preprocess_only, skip_schemas)
-    if loadingContext.do_update in (True, None):
-        fileuri = urllib.parse.urldefrag(uri)[0]
-        def update_index(pr):
-            loadingContext.loader.idx[pr["id"]] = pr
-        visit_class(loadingContext.loader.idx[fileuri], ("CommandLineTool", "Workflow", "ExpressionTool"), update_index)
-    return loadingContext, uri
-cwltool.load_tool.resolve_and_validate_document = wrapped_resolve_and_validate_document
-### end monkey patch ###
-
 from schema_salad.sourceline import SourceLine
 import schema_salad.validate as validate
 import cwltool.main
@@ -60,7 +23,7 @@ import cwltool.workflow
 import cwltool.process
 import cwltool.argparser
 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing
+from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing
 
 import arvados
 import arvados.config
@@ -213,7 +176,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     parser.add_argument("--enable-dev", action="store_true",
                         help="Enable loading and running development versions "
-                             "of CWL spec.", default=False)
+                             "of the CWL standards.", default=False)
     parser.add_argument('--storage-classes', default="default",
                         help="Specify comma separated list of storage classes to be used when saving workflow output to Keep.")
 
@@ -257,8 +220,8 @@ def add_arv_hints():
     cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
     res10 = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.0.yml')
     res11 = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.1.yml')
-    customschema10 = res10.read()
-    customschema11 = res11.read()
+    customschema10 = res10.read().decode('utf-8')
+    customschema11 = res11.read().decode('utf-8')
     use_custom_schema("v1.0", "http://arvados.org/cwl", customschema10)
     use_custom_schema("v1.1.0-dev1", "http://arvados.org/cwl", customschema11)
     use_custom_schema("v1.1", "http://arvados.org/cwl", customschema11)