Merge branch '19688-cwl-fast-path' refs #19688

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 08a05d571cb8e41bb48265489fcec9f13b1e6100..9cad9bd00d11eb96f50d2a65be5961de06e4d8c6 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -36,6 +36,7 @@ from arvados.api import OrderedJsonModel
 from .perf import Perf
 from ._version import __version__
 from .executor import ArvCwlExecutor
+from .fsaccess import workflow_uuid_pattern
 
 # These aren't used directly in this file but
 # other code expects to import them from here
@@ -199,6 +200,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         action="store_false", default=True,
                         help=argparse.SUPPRESS)
 
+    parser.add_argument("--disable-git", dest="git_info",
+                        action="store_false", default=True,
+                        help=argparse.SUPPRESS)
+
     parser.add_argument("--disable-color", dest="enable_color",
                         action="store_false", default=True,
                         help=argparse.SUPPRESS)
@@ -359,6 +364,10 @@ def main(args=sys.argv[1:],
         # unit tests.
         stdout = None
 
+    if arvargs.submit and (arvargs.workflow.startswith("arvwf:") or workflow_uuid_pattern.match(arvargs.workflow)):
+        executor.loadingContext.do_validate = False
+        executor.fast_submit = True
+
     return cwltool.main.main(args=arvargs,
                              stdout=stdout,
                              stderr=stderr,

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 66fe143e0f42d169d29ec04e85ddd50a6702f1c9..57ab7367a34bb2a176454ed42a9f98aaae71f166 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -523,6 +523,15 @@ class RunnerContainer(Runner):
                 "kind": "collection",
                 "portable_data_hash": "%s" % workflowcollection
             }
+        elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
+            workflowpath = "/var/lib/cwl/workflow.json#main"
+            record = self.arvrunner.api.workflows().get(uuid=self.embedded_tool.tool["id"][6:33]).execute(num_retries=self.arvrunner.num_retries)
+            packed = yaml.safe_load(record["definition"])
+            container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
+                "kind": "json",
+                "content": packed
+            }
+            container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
         else:
             packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext, git_info)
             workflowpath = "/var/lib/cwl/workflow.json#main"
@@ -530,8 +539,6 @@ class RunnerContainer(Runner):
                 "kind": "json",
                 "content": packed
             }
-            if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
-                container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 
         container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
 

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 5f3feabf8c83271ccec89d667d296663b86fecfa..56226388d7ab36618d1ff354c70d6bf512c18cea 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -13,6 +13,8 @@ import logging
 from schema_salad.sourceline import SourceLine, cmap
 import schema_salad.ref_resolver
 
+import arvados.collection
+
 from cwltool.pack import pack
 from cwltool.load_tool import fetch_document, resolve_and_validate_document
 from cwltool.process import shortname
@@ -37,6 +39,84 @@ metrics = logging.getLogger('arvados.cwl-runner.metrics')
 max_res_pars = ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax")
 sum_res_pars = ("outdirMin", "outdirMax")
 
+def make_wrapper_workflow(arvRunner, main, packed, project_uuid, name, git_info, tool):
+    col = arvados.collection.Collection(api_client=arvRunner.api,
+                                        keep_client=arvRunner.keep_client)
+
+    with col.open("workflow.json", "wt") as f:
+        json.dump(packed, f, sort_keys=True, indent=4, separators=(',',': '))
+
+    pdh = col.portable_data_hash()
+
+    toolname = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
+    if git_info and git_info.get("http://arvados.org/cwl#gitDescribe"):
+        toolname = "%s (%s)" % (toolname, git_info.get("http://arvados.org/cwl#gitDescribe"))
+
+    existing = arvRunner.api.collections().list(filters=[["portable_data_hash", "=", pdh], ["owner_uuid", "=", project_uuid]]).execute(num_retries=arvRunner.num_retries)
+    if len(existing["items"]) == 0:
+        col.save_new(name=toolname, owner_uuid=project_uuid, ensure_unique_name=True)
+
+    # now construct the wrapper
+
+    step = {
+        "id": "#main/" + toolname,
+        "in": [],
+        "out": [],
+        "run": "keep:%s/workflow.json#main" % pdh,
+        "label": name
+    }
+
+    newinputs = []
+    for i in main["inputs"]:
+        inp = {}
+        # Make sure to only copy known fields that are meaningful at
+        # the workflow level. In practice this ensures that if we're
+        # wrapping a CommandLineTool we don't grab inputBinding.
+        # Right now also excludes extension fields, which is fine,
+        # Arvados doesn't currently look for any extension fields on
+        # input parameters.
+        for f in ("type", "label", "secondaryFiles", "streamable",
+                  "doc", "id", "format", "loadContents",
+                  "loadListing", "default"):
+            if f in i:
+                inp[f] = i[f]
+        newinputs.append(inp)
+
+    wrapper = {
+        "class": "Workflow",
+        "id": "#main",
+        "inputs": newinputs,
+        "outputs": [],
+        "steps": [step]
+    }
+
+    for i in main["inputs"]:
+        step["in"].append({
+            "id": "#main/step/%s" % shortname(i["id"]),
+            "source": i["id"]
+        })
+
+    for i in main["outputs"]:
+        step["out"].append({"id": "#main/step/%s" % shortname(i["id"])})
+        wrapper["outputs"].append({"outputSource": "#main/step/%s" % shortname(i["id"]),
+                                   "type": i["type"],
+                                   "id": i["id"]})
+
+    wrapper["requirements"] = [{"class": "SubworkflowFeatureRequirement"}]
+
+    if main.get("requirements"):
+        wrapper["requirements"].extend(main["requirements"])
+    if main.get("hints"):
+        wrapper["hints"] = main["hints"]
+
+    doc = {"cwlVersion": "v1.2", "$graph": [wrapper]}
+
+    if git_info:
+        for g in git_info:
+            doc[g] = git_info[g]
+
+    return json.dumps(doc, sort_keys=True, indent=4, separators=(',',': '))
+
 def upload_workflow(arvRunner, tool, job_order, project_uuid,
                     runtimeContext, uuid=None,
                     submit_runner_ram=0, name=None, merged_map=None,
@@ -84,11 +164,13 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid,
 
     main["hints"] = hints
 
+    wrapper = make_wrapper_workflow(arvRunner, main, packed, project_uuid, name, git_info, tool)
+
     body = {
         "workflow": {
             "name": name,
             "description": tool.tool.get("doc", ""),
-            "definition":json.dumps(packed, sort_keys=True, indent=4, separators=(',',': '))
+            "definition": wrapper
         }}
     if project_uuid:
         body["workflow"]["owner_uuid"] = project_uuid
@@ -147,8 +229,13 @@ class ArvadosWorkflowStep(WorkflowStep):
                  **argv
                 ):  # type: (...) -> None
 
-        super(ArvadosWorkflowStep, self).__init__(toolpath_object, pos, loadingContext, *argc, **argv)
-        self.tool["class"] = "WorkflowStep"
+        if arvrunner.fast_submit:
+            self.tool = toolpath_object
+            self.tool["inputs"] = []
+            self.tool["outputs"] = []
+        else:
+            super(ArvadosWorkflowStep, self).__init__(toolpath_object, pos, loadingContext, *argc, **argv)
+            self.tool["class"] = "WorkflowStep"
         self.arvrunner = arvrunner
 
     def job(self, joborder, output_callback, runtimeContext):

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 694f77baf246ecb56e6116e99dd5461deb9f6e53..a30c0fff5d316c25e867a077819e04f83f5554cc 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -112,6 +112,7 @@ class ArvCwlExecutor(object):
             arvargs.output_tags = None
             arvargs.thread_count = 1
             arvargs.collection_cache_size = None
+            arvargs.git_info = True
 
         self.api = api_client
         self.processes = {}
@@ -137,6 +138,8 @@ class ArvCwlExecutor(object):
         self.fs_access = None
         self.secret_store = None
         self.stdout = stdout
+        self.fast_submit = False
+        self.git_info = arvargs.git_info
 
         if keep_client is not None:
             self.keep_client = keep_client
@@ -582,7 +585,7 @@ The 'jobs' API is no longer supported.
     def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
         self.debug = runtimeContext.debug
 
-        git_info = self.get_git_info(updated_tool)
+        git_info = self.get_git_info(updated_tool) if self.git_info else {}
         if git_info:
             logger.info("Git provenance")
             for g in git_info:
@@ -594,7 +597,8 @@ The 'jobs' API is no longer supported.
         controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
         logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], workbench2 or workbench1 or controller)
 
-        updated_tool.visit(self.check_features)
+        if not self.fast_submit:
+            updated_tool.visit(self.check_features)
 
         self.pipeline = None
         self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir)
@@ -662,7 +666,7 @@ The 'jobs' API is no longer supported.
         loadingContext = self.loadingContext.copy()
         loadingContext.do_validate = False
         loadingContext.disable_js_validation = True
-        if submitting:
+        if submitting and not self.fast_submit:
             loadingContext.do_update = False
             # Document may have been auto-updated. Reload the original
             # document with updating disabled because we want to
@@ -675,9 +679,12 @@ The 'jobs' API is no longer supported.
 
         # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
         # Also uploads docker images.
-        logger.info("Uploading workflow dependencies")
-        with Perf(metrics, "upload_workflow_deps"):
-            merged_map = upload_workflow_deps(self, tool, runtimeContext)
+        if not self.fast_submit:
+            logger.info("Uploading workflow dependencies")
+            with Perf(metrics, "upload_workflow_deps"):
+                merged_map = upload_workflow_deps(self, tool, runtimeContext)
+        else:
+            merged_map = {}
 
         # Recreate process object (ArvadosWorkflow or
         # ArvadosCommandTool) because tool document may have been

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 4da8f855692aed44f212739d5e515af3fef2ceb0..5c09e671fa21eac1952c417e10580d332e3612be 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -244,10 +244,11 @@ class CollectionFetcher(DefaultFetcher):
         try:
             if url.startswith("http://arvados.org/cwl"):
                 return True
-            if url.startswith("keep:"):
-                return self.fsaccess.exists(url)
-            if url.startswith("arvwf:"):
-                if self.fetch_text(url):
+            urld, _ = urllib.parse.urldefrag(url)
+            if urld.startswith("keep:"):
+                return self.fsaccess.exists(urld)
+            if urld.startswith("arvwf:"):
+                if self.fetch_text(urld):
                     return True
         except arvados.errors.NotFoundError:
             return False

diff --git a/sdk/cwl/tests/collection_per_tool/collection_per_tool_wrapper.cwl b/sdk/cwl/tests/collection_per_tool/collection_per_tool_wrapper.cwl
new file mode 100644 (file)
index 0000000..fda566c
--- /dev/null
+++ b/sdk/cwl/tests/collection_per_tool/collection_per_tool_wrapper.cwl
@@ -0,0 +1,35 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+{
+    "$graph": [
+        {
+            "class": "Workflow",
+            "hints": [
+                {
+                    "acrContainerImage": "999999999999999999999999999999d3+99",
+                    "class": "http://arvados.org/cwl#WorkflowRunnerResources"
+                }
+            ],
+            "id": "#main",
+            "inputs": [],
+            "outputs": [],
+            "requirements": [
+                {
+                    "class": "SubworkflowFeatureRequirement"
+                }
+            ],
+            "steps": [
+                {
+                    "id": "#main/collection_per_tool.cwl",
+                    "in": [],
+                    "label": "collection_per_tool.cwl",
+                    "out": [],
+                    "run": "keep:92045991f69a417f2f26660db67911ef+61/workflow.json#main"
+                }
+            ]
+        }
+    ],
+    "cwlVersion": "v1.2"
+}

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index b44f6feb5d28db91d38bcc25105c5b2adc513b95..17c09f1ee78db4c5a1b45b1d71769f33d71fd8d7 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -290,13 +290,13 @@ def stubs(wfdetails=('submit_wf.cwl', None)):
             gitinfo_workflow["$graph"][0]["id"] = "file://%s/tests/wf/%s" % (cwd, wfpath)
             mocktool = mock.NonCallableMock(tool=gitinfo_workflow["$graph"][0], metadata=gitinfo_workflow)
 
-            git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool)
-            expect_packed_workflow.update(git_info)
+            stubs.git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool)
+            expect_packed_workflow.update(stubs.git_info)
 
-            git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in git_info.items()}
+            stubs.git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in stubs.git_info.items()}
 
             if wfname == wfpath:
-                container_name = "%s (%s)" % (wfpath, git_props["arv:gitDescribe"])
+                container_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"])
             else:
                 container_name = wfname
 
@@ -359,7 +359,7 @@ def stubs(wfdetails=('submit_wf.cwl', None)):
                     'ram': (1024+256)*1024*1024
                 },
                 'use_existing': False,
-                'properties': git_props,
+                'properties': stubs.git_props,
                 'secret_mounts': {}
             }
 
@@ -393,7 +393,7 @@ class TestSubmit(unittest.TestCase):
         root_logger.handlers = handlers
 
     @mock.patch("time.sleep")
-    @stubs
+    @stubs()
     def test_submit_invalid_runner_ram(self, stubs, tm):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
@@ -402,7 +402,7 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(exited, 1)
 
 
-    @stubs
+    @stubs()
     def test_submit_container(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug",
@@ -414,7 +414,7 @@ class TestSubmit(unittest.TestCase):
                 'manifest_text':
                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
                 'replication_desired': None,
-                'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
+                'name': 'submit_wf.cwl ('+ stubs.git_props["arv:gitDescribe"] +') input (169f39d466a5438ac4a90e779bf750c7+53)',
             }), ensure_unique_name=False),
             mock.call(body=JsonDiffMatcher({
                 'manifest_text':
@@ -432,7 +432,7 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(exited, 0)
 
 
-    @stubs
+    @stubs()
     def test_submit_container_tool(self, stubs):
         # test for issue #16139
         exited = arvados_cwl.main(
@@ -444,7 +444,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_no_reuse(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
@@ -457,7 +457,7 @@ class TestSubmit(unittest.TestCase):
             '--no-log-timestamps', '--disable-validate', '--disable-color',
             '--eval-timeout=20', '--thread-count=0',
             '--disable-reuse', "--collection-cache-size=256",
-            "--output-name=Output from workflow submit_wf.cwl",
+            '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
             '--debug', '--on-error=continue',
             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
         expect_container["use_existing"] = False
@@ -496,7 +496,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
 
 
-    @stubs
+    @stubs()
     def test_submit_container_on_error(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
@@ -508,7 +508,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=stop',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
@@ -518,7 +518,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_output_name(self, stubs):
         output_name = "test_output_name"
 
@@ -542,7 +542,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_storage_classes(self, stubs):
         exited = arvados_cwl.main(
             ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
@@ -554,7 +554,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       '--output-name=Output from workflow submit_wf.cwl',
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        "--debug",
                                        "--storage-classes=foo", '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -565,7 +565,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_multiple_storage_classes(self, stubs):
         exited = arvados_cwl.main(
             ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
@@ -577,7 +577,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        "--debug",
                                        "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -591,7 +591,7 @@ class TestSubmit(unittest.TestCase):
     @mock.patch("cwltool.task_queue.TaskQueue")
     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
-    @stubs
+    @stubs()
     def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
         final_output_c = arvados.collection.Collection()
         make_output.return_value = ({},final_output_c)
@@ -602,17 +602,17 @@ class TestSubmit(unittest.TestCase):
         job.side_effect = set_final_output
 
         exited = arvados_cwl.main(
-            ["--debug", "--local", "--storage-classes=foo",
+            ["--debug", "--local", "--storage-classes=foo", "--disable-git",
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
-        make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
+        make_output.assert_called_with(u'Output from workflow submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
         self.assertEqual(exited, 0)
 
     @mock.patch("cwltool.task_queue.TaskQueue")
     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
-    @stubs
+    @stubs()
     def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
         final_output_c = arvados.collection.Collection()
         make_output.return_value = ({},final_output_c)
@@ -624,17 +624,17 @@ class TestSubmit(unittest.TestCase):
         job.side_effect = set_final_output
 
         exited = arvados_cwl.main(
-            ["--debug", "--local",
+            ["--debug", "--local", "--disable-git",
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
-        make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
+        make_output.assert_called_with(u'Output from workflow submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
         self.assertEqual(exited, 0)
 
     @mock.patch("cwltool.task_queue.TaskQueue")
     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
-    @stubs
+    @stubs()
     def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
         final_output_c = arvados.collection.Collection()
         make_output.return_value = ({},final_output_c)
@@ -645,14 +645,14 @@ class TestSubmit(unittest.TestCase):
         job.side_effect = set_final_output
 
         exited = arvados_cwl.main(
-            ["--debug", "--local",
+            ["--debug", "--local", "--disable-git",
                 "tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
-        make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
+        make_output.assert_called_with(u'Output from workflow submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_output_ttl(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
@@ -664,7 +664,8 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl", '--debug',
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug',
                                        '--on-error=continue',
                                        "--intermediate-output-ttl=3600",
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -675,7 +676,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_trash_intermediate(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
@@ -688,6 +689,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=continue',
                                        "--trash-intermediate",
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -698,7 +700,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_output_tags(self, stubs):
         output_tags = "tag0,tag1,tag2"
 
@@ -712,7 +714,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        "--output-tags="+output_tags, '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
@@ -722,7 +724,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_runner_ram(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
@@ -740,7 +742,7 @@ class TestSubmit(unittest.TestCase):
 
     @mock.patch("arvados.collection.CollectionReader")
     @mock.patch("time.sleep")
-    @stubs
+    @stubs()
     def test_submit_file_keepref(self, stubs, tm, collectionReader):
         collectionReader().exists.return_value = True
         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
@@ -752,7 +754,7 @@ class TestSubmit(unittest.TestCase):
 
     @mock.patch("arvados.collection.CollectionReader")
     @mock.patch("time.sleep")
-    @stubs
+    @stubs()
     def test_submit_keepref(self, stubs, tm, reader):
         with open("tests/wf/expect_arvworkflow.cwl") as f:
             reader().open().__enter__().read.return_value = f.read()
@@ -813,13 +815,13 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(exited, 0)
 
     @mock.patch("time.sleep")
-    @stubs
+    @stubs()
     def test_submit_arvworkflow(self, stubs, tm):
         with open("tests/wf/expect_arvworkflow.cwl") as f:
             stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
 
         exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--api=containers", "--debug",
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-git",
              "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -863,8 +865,7 @@ class TestSubmit(unittest.TestCase):
                                 'requirements': [
                                     {
                                         'dockerPull': 'debian:buster-slim',
-                                        'class': 'DockerRequirement',
-                                        "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
+                                        'class': 'DockerRequirement'
                                     }
                                 ],
                                 'id': '#submit_tool.cwl',
@@ -888,8 +889,11 @@ class TestSubmit(unittest.TestCase):
             'command': ['arvados-cwl-runner', '--local', '--api=containers',
                         '--no-log-timestamps', '--disable-validate', '--disable-color',
                         '--eval-timeout=20', '--thread-count=0',
-                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                        '--enable-reuse', "--collection-cache-size=256",
+                        "--output-name=Output from workflow a test workflow",
+                        '--debug', '--on-error=continue',
                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+            'output_name': 'Output from workflow a test workflow',
             'cwd': '/var/spool/cwl',
             'runtime_constraints': {
                 'API': True,
@@ -924,7 +928,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_missing_input(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug",
@@ -938,7 +942,7 @@ class TestSubmit(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
         self.assertEqual(exited, 1)
 
-    @stubs
+    @stubs()
     def test_submit_container_project(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -953,7 +957,8 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        "--eval-timeout=20", "--thread-count=0",
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl", '--debug',
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug',
                                        '--on-error=continue',
                                        '--project-uuid='+project_uuid,
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -964,7 +969,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_eval_timeout(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
@@ -976,6 +981,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=60.0', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
@@ -985,7 +991,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_collection_cache(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
@@ -997,6 +1003,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=500",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
         expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024
@@ -1007,7 +1014,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_thread_count(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
@@ -1019,6 +1026,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=20',
                                        '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
@@ -1028,7 +1036,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_runner_image(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
@@ -1044,7 +1052,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_priority(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
@@ -1148,13 +1156,16 @@ class TestSubmit(unittest.TestCase):
                          arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__, arvrunner.runtimeContext))
 
 
-    @stubs
+    @stubs()
     def test_submit_secrets(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug",
                 "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
+        stubs.git_props["arv:gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl"
+        stubs.git_info["http://arvados.org/cwl#gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl"
+
         expect_container = {
             "command": [
                 "arvados-cwl-runner",
@@ -1167,8 +1178,8 @@ class TestSubmit(unittest.TestCase):
                 '--thread-count=0',
                 "--enable-reuse",
                 "--collection-cache-size=256",
-                '--output-name=Output from workflow secret_wf.cwl'
-                '--debug',
+                '--output-name=Output from workflow secret_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                "--debug",
                 "--on-error=continue",
                 "/var/lib/cwl/workflow.json#main",
                 "/var/lib/cwl/cwl.input.json"
@@ -1292,11 +1303,11 @@ class TestSubmit(unittest.TestCase):
                     "path": "/var/spool/cwl/cwl.output.json"
                 }
             },
-            "name": "secret_wf.cwl",
-            "output_name": "Output from workflow secret_wf.cwl",
+            "name": "secret_wf.cwl (%s)" % stubs.git_props["arv:gitDescribe"],
+            "output_name": "Output from workflow secret_wf.cwl (%s)" % stubs.git_props["arv:gitDescribe"],
             "output_path": "/var/spool/cwl",
             "priority": 500,
-            "properties": {},
+            "properties": stubs.git_props,
             "runtime_constraints": {
                 "API": True,
                 "ram": 1342177280,
@@ -1312,13 +1323,15 @@ class TestSubmit(unittest.TestCase):
             "use_existing": False
         }
 
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"].update(stubs.git_info)
+
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
         self.assertEqual(stubs.capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_request_uuid(self, stubs):
         stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
         stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
@@ -1340,7 +1353,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_cluster_id(self, stubs):
         stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
 
@@ -1357,7 +1370,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_validate_cluster_id(self, stubs):
         stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
         exited = arvados_cwl.main(
@@ -1366,7 +1379,7 @@ class TestSubmit(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
         self.assertEqual(exited, 1)
 
-    @stubs
+    @stubs()
     def test_submit_validate_project_uuid(self, stubs):
         # Fails with bad cluster prefix
         exited = arvados_cwl.main(
@@ -1392,7 +1405,7 @@ class TestSubmit(unittest.TestCase):
 
 
     @mock.patch("arvados.collection.CollectionReader")
-    @stubs
+    @stubs()
     def test_submit_uuid_inputs(self, stubs, collectionReader):
         collectionReader().exists.return_value = True
         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
@@ -1427,7 +1440,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_mismatched_uuid_inputs(self, stubs):
         def list_side_effect(**kwargs):
             m = mock.MagicMock()
@@ -1460,7 +1473,7 @@ class TestSubmit(unittest.TestCase):
                 cwltool_logger.removeHandler(stderr_logger)
 
     @mock.patch("arvados.collection.CollectionReader")
-    @stubs
+    @stubs()
     def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
         capture_stderr = StringIO()
@@ -1528,7 +1541,7 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(exited, 0)
 
 
-    @stubs
+    @stubs()
     def test_submit_enable_preemptible(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
@@ -1537,11 +1550,13 @@ class TestSubmit(unittest.TestCase):
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
-                        '--no-log-timestamps', '--disable-validate', '--disable-color',
-                        '--eval-timeout=20', '--thread-count=0',
-                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
+                                       '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug', '--on-error=continue',
                                        '--enable-preemptible',
-                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
@@ -1549,7 +1564,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_disable_preemptible(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
@@ -1558,11 +1573,13 @@ class TestSubmit(unittest.TestCase):
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
-                        '--no-log-timestamps', '--disable-validate', '--disable-color',
-                        '--eval-timeout=20', '--thread-count=0',
-                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
+                                       '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug', '--on-error=continue',
                                        '--disable-preemptible',
-                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
@@ -1574,7 +1591,9 @@ class TestSubmit(unittest.TestCase):
 class TestCreateWorkflow(unittest.TestCase):
     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
     expect_workflow = StripYAMLComments(
-        open("tests/wf/expect_upload_packed.cwl").read().rstrip())
+        open("tests/wf/expect_upload_wrapper.cwl").read().rstrip())
+    expect_workflow_altname = StripYAMLComments(
+        open("tests/wf/expect_upload_wrapper_altname.cwl").read().rstrip())
 
     def setUp(self):
         cwltool.process._names = set()
@@ -1587,7 +1606,7 @@ class TestCreateWorkflow(unittest.TestCase):
         handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
         root_logger.handlers = handlers
 
-    @stubs
+    @stubs()
     def test_create(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -1596,6 +1615,7 @@ class TestCreateWorkflow(unittest.TestCase):
             ["--create-workflow", "--debug",
              "--api=containers",
              "--project-uuid", project_uuid,
+             "--disable-git",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -1617,7 +1637,7 @@ class TestCreateWorkflow(unittest.TestCase):
                          stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_create_name(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -1627,6 +1647,7 @@ class TestCreateWorkflow(unittest.TestCase):
              "--api=containers",
              "--project-uuid", project_uuid,
              "--name", "testing 123",
+             "--disable-git",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -1638,7 +1659,7 @@ class TestCreateWorkflow(unittest.TestCase):
                 "owner_uuid": project_uuid,
                 "name": "testing 123",
                 "description": "",
-                "definition": self.expect_workflow,
+                "definition": self.expect_workflow_altname,
             }
         }
         stubs.api.workflows().create.assert_called_with(
@@ -1649,7 +1670,7 @@ class TestCreateWorkflow(unittest.TestCase):
         self.assertEqual(exited, 0)
 
 
-    @stubs
+    @stubs()
     def test_update(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
@@ -1657,6 +1678,7 @@ class TestCreateWorkflow(unittest.TestCase):
         exited = arvados_cwl.main(
             ["--update-workflow", self.existing_workflow_uuid,
              "--debug",
+             "--disable-git",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -1676,7 +1698,7 @@ class TestCreateWorkflow(unittest.TestCase):
         self.assertEqual(exited, 0)
 
 
-    @stubs
+    @stubs()
     def test_update_name(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
@@ -1684,6 +1706,7 @@ class TestCreateWorkflow(unittest.TestCase):
         exited = arvados_cwl.main(
             ["--update-workflow", self.existing_workflow_uuid,
              "--debug", "--name", "testing 123",
+             "--disable-git",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -1691,7 +1714,7 @@ class TestCreateWorkflow(unittest.TestCase):
             "workflow": {
                 "name": "testing 123",
                 "description": "",
-                "definition": self.expect_workflow,
+                "definition": self.expect_workflow_altname,
                 "owner_uuid": project_uuid
             }
         }
@@ -1702,7 +1725,7 @@ class TestCreateWorkflow(unittest.TestCase):
                          self.existing_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_create_collection_per_tool(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -1711,10 +1734,11 @@ class TestCreateWorkflow(unittest.TestCase):
             ["--create-workflow", "--debug",
              "--api=containers",
              "--project-uuid", project_uuid,
+             "--disable-git",
              "tests/collection_per_tool/collection_per_tool.cwl"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
-        toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
+        toolfile = "tests/collection_per_tool/collection_per_tool_wrapper.cwl"
         expect_workflow = StripYAMLComments(open(toolfile).read().rstrip())
 
         body = {
@@ -1732,7 +1756,7 @@ class TestCreateWorkflow(unittest.TestCase):
                          stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_create_with_imports(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -1751,7 +1775,7 @@ class TestCreateWorkflow(unittest.TestCase):
                          stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_create_with_no_input(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}

diff --git a/sdk/cwl/tests/wf/expect_upload_wrapper.cwl b/sdk/cwl/tests/wf/expect_upload_wrapper.cwl
new file mode 100644 (file)
index 0000000..3821527
--- /dev/null
+++ b/sdk/cwl/tests/wf/expect_upload_wrapper.cwl
@@ -0,0 +1,89 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+{
+    "$graph": [
+        {
+            "class": "Workflow",
+            "hints": [
+                {
+                    "acrContainerImage": "999999999999999999999999999999d3+99",
+                    "class": "http://arvados.org/cwl#WorkflowRunnerResources"
+                }
+            ],
+            "id": "#main",
+            "inputs": [
+                {
+                    "default": {
+                        "basename": "blorp.txt",
+                        "class": "File",
+                        "location": "keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt",
+                        "nameext": ".txt",
+                        "nameroot": "blorp",
+                        "size": 16
+                    },
+                    "id": "#main/x",
+                    "type": "File"
+                },
+                {
+                    "default": {
+                        "basename": "99999999999999999999999999999998+99",
+                        "class": "Directory",
+                        "location": "keep:99999999999999999999999999999998+99"
+                    },
+                    "id": "#main/y",
+                    "type": "Directory"
+                },
+                {
+                    "default": {
+                        "basename": "anonymous",
+                        "class": "Directory",
+                        "listing": [
+                            {
+                                "basename": "renamed.txt",
+                                "class": "File",
+                                "location": "keep:99999999999999999999999999999998+99/file1.txt",
+                                "nameext": ".txt",
+                                "nameroot": "renamed",
+                                "size": 0
+                            }
+                        ],
+                        "location": "_:df80736f-f14d-4b10-b2e3-03aa27f034b2"
+                    },
+                    "id": "#main/z",
+                    "type": "Directory"
+                }
+            ],
+            "outputs": [],
+            "requirements": [
+                {
+                    "class": "SubworkflowFeatureRequirement"
+                }
+            ],
+            "steps": [
+                {
+                    "id": "#main/submit_wf.cwl",
+                    "in": [
+                        {
+                            "id": "#main/step/x",
+                            "source": "#main/x"
+                        },
+                        {
+                            "id": "#main/step/y",
+                            "source": "#main/y"
+                        },
+                        {
+                            "id": "#main/step/z",
+                            "source": "#main/z"
+                        }
+                    ],
+                    "label": "submit_wf.cwl",
+                    "out": [],
+                    "run": "keep:f1c2b0c514a5fb9b2a8b5b38a31bab66+61/workflow.json#main"
+                }
+            ]
+        }
+    ],
+    "cwlVersion": "v1.2"
+}

diff --git a/sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl b/sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl
new file mode 100644 (file)
index 0000000..d486e5a
--- /dev/null
+++ b/sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl
@@ -0,0 +1,89 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+{
+    "$graph": [
+        {
+            "class": "Workflow",
+            "hints": [
+                {
+                    "acrContainerImage": "999999999999999999999999999999d3+99",
+                    "class": "http://arvados.org/cwl#WorkflowRunnerResources"
+                }
+            ],
+            "id": "#main",
+            "inputs": [
+                {
+                    "default": {
+                        "basename": "blorp.txt",
+                        "class": "File",
+                        "location": "keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt",
+                        "nameext": ".txt",
+                        "nameroot": "blorp",
+                        "size": 16
+                    },
+                    "id": "#main/x",
+                    "type": "File"
+                },
+                {
+                    "default": {
+                        "basename": "99999999999999999999999999999998+99",
+                        "class": "Directory",
+                        "location": "keep:99999999999999999999999999999998+99"
+                    },
+                    "id": "#main/y",
+                    "type": "Directory"
+                },
+                {
+                    "default": {
+                        "basename": "anonymous",
+                        "class": "Directory",
+                        "listing": [
+                            {
+                                "basename": "renamed.txt",
+                                "class": "File",
+                                "location": "keep:99999999999999999999999999999998+99/file1.txt",
+                                "nameext": ".txt",
+                                "nameroot": "renamed",
+                                "size": 0
+                            }
+                        ],
+                        "location": "_:df80736f-f14d-4b10-b2e3-03aa27f034b2"
+                    },
+                    "id": "#main/z",
+                    "type": "Directory"
+                }
+            ],
+            "outputs": [],
+            "requirements": [
+                {
+                    "class": "SubworkflowFeatureRequirement"
+                }
+            ],
+            "steps": [
+                {
+                    "id": "#main/submit_wf.cwl",
+                    "in": [
+                        {
+                            "id": "#main/step/x",
+                            "source": "#main/x"
+                        },
+                        {
+                            "id": "#main/step/y",
+                            "source": "#main/y"
+                        },
+                        {
+                            "id": "#main/step/z",
+                            "source": "#main/z"
+                        }
+                    ],
+                    "label": "testing 123",
+                    "out": [],
+                    "run": "keep:f1c2b0c514a5fb9b2a8b5b38a31bab66+61/workflow.json#main"
+                }
+            ]
+        }
+    ],
+    "cwlVersion": "v1.2"
+}