From 1d9e4de7a4ff994cfc7a9319dcae56bb26c272b3 Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Fri, 28 Feb 2020 12:07:35 -0500
Subject: [PATCH] 16169: Monkey patch load_tool.resolve_and_validate_document
 to fix bug

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.
---
 sdk/cwl/arvados_cwl/__init__.py           | 37 +++++++++++++++++++++++
 sdk/cwl/tests/wf/16169-step.cwl           |  4 ++-
 sdk/python/arvados/commands/keepdocker.py |  2 +-
 3 files changed, 41 insertions(+), 2 deletions(-)

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 3dd04040ab..2b2acd5688 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -16,6 +16,43 @@ 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
diff --git a/sdk/cwl/tests/wf/16169-step.cwl b/sdk/cwl/tests/wf/16169-step.cwl
index 8386df517b..ce6f2c0c93 100644
--- a/sdk/cwl/tests/wf/16169-step.cwl
+++ b/sdk/cwl/tests/wf/16169-step.cwl
@@ -6,10 +6,12 @@ class: CommandLineTool
 cwlVersion: v1.0
 requirements:
   InlineJavascriptRequirement: {}
+  DockerRequirement:
+    dockerPull: debian:stretch-slim
 inputs:
   d: Directory
 outputs:
   out: stdout
 stdout: output.txt
 arguments:
-  [echo, "${if(inputs.d.listing === undefined) {return 'true';} else {return 'false';}}"]
\ No newline at end of file
+  [echo, "${if(inputs.d.listing === undefined) {return 'true';} else {return 'false';}}"]
diff --git a/sdk/python/arvados/commands/keepdocker.py b/sdk/python/arvados/commands/keepdocker.py
index c89fa644cc..6673888ab5 100644
--- a/sdk/python/arvados/commands/keepdocker.py
+++ b/sdk/python/arvados/commands/keepdocker.py
@@ -390,7 +390,7 @@ def main(arguments=None, stdout=sys.stdout, install_sig_handlers=True, api=None)
     try:
         image_hash = find_one_image_hash(args.image, args.tag)
     except DockerError as error:
-        logger.error(error.message)
+        logger.error(str(error))
         sys.exit(1)
 
     if not docker_image_compatible(api, image_hash):
-- 
2.30.2