[ARVADOS] updated: 1.3.0-2262-g60ed2df38

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvworkflow.py  |  2 +-
 sdk/cwl/arvados_cwl/runner.py       |  5 +++--
 sdk/cwl/setup.py                    |  2 +-
 sdk/cwl/tests/test_container.py     |  6 +++---
 sdk/cwl/tests/wf/scatter2_subwf.cwl | 15 +++++++++------
 5 files changed, 17 insertions(+), 13 deletions(-)

       via  60ed2df387ca0ee304bf8d2e40f2199184375b29 (commit)
      from  cf447c1718535fe924005db53bed5011c714dd63 (commit)

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commit 60ed2df387ca0ee304bf8d2e40f2199184375b29
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Tue Mar 17 17:08:44 2020 -0400

    12409: Bump cwltool version for more bugfixing.
    
    The tests pass, and the tests confirm that the packed workflow is the
    original version and not the upgraded version, which is what we
    wanted.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index ba6033364..ddd3c0076 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -186,7 +186,7 @@ class ArvadosWorkflow(Workflow):
                                 False)
 
             if self.wf_pdh is None:
-                packed = pack(self.doc_loader, self.tool, self.tool["id"], self.metadata)
+                packed = pack(self.loadingContext, self.tool["id"], loader=self.doc_loader)
 
                 for p in packed["$graph"]:
                     if p["id"] == "#main":
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 2239e0f9d..f0be83032 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -424,8 +424,9 @@ def packed_workflow(arvrunner, tool, merged_map):
     A "packed" workflow is one where all the components have been combined into a single document."""
 
     rewrites = {}
-    packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]),
-                  tool.tool["id"], tool.metadata, rewrite_out=rewrites)
+    packed = pack(arvrunner.loadingContext, tool.tool["id"],
+                  rewrite_out=rewrites,
+                  loader=tool.doc_loader)
 
     rewrite_to_orig = {v: k for k,v in viewitems(rewrites)}
 
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 5a359d22c..95730a69b 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -39,7 +39,7 @@ setup(name='arvados-cwl-runner',
       # file to determine what version of cwltool and schema-salad to
       # build.
       install_requires=[
-          'cwltool==2.0.20200312183052',
+          'cwltool==3.0.20200317203547',
           'schema-salad==5.0.20200302192450',
           'arvados-python-client{}'.format(pysdk_dep),
           'setuptools',
diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index 8677db92a..d331e3552 100644
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -849,7 +849,7 @@ class TestWorkflow(unittest.TestCase):
         cwltool.process._names = set()
 
     def helper(self, runner, enable_reuse=True):
-        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
+        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -929,7 +929,7 @@ class TestWorkflow(unittest.TestCase):
                     "--no-container",
                     "--move-outputs",
                     "--preserve-entire-environment",
-                    "workflow.cwl#main",
+                    "workflow.cwl",
                     "cwl.input.yml"
                 ],
                 "container_image": "99999999999999999999999999999993+99",
@@ -1077,7 +1077,7 @@ class TestWorkflow(unittest.TestCase):
                     u'--no-container',
                     u'--move-outputs',
                     u'--preserve-entire-environment',
-                    u'workflow.cwl#main',
+                    u'workflow.cwl',
                     u'cwl.input.yml'
                 ],
                 'use_existing': True,
diff --git a/sdk/cwl/tests/wf/scatter2_subwf.cwl b/sdk/cwl/tests/wf/scatter2_subwf.cwl
index 035c1e97e..c54e1707f 100644
--- a/sdk/cwl/tests/wf/scatter2_subwf.cwl
+++ b/sdk/cwl/tests/wf/scatter2_subwf.cwl
@@ -5,8 +5,11 @@
 {
   "$graph": [
     {
+      "$namespaces": {
+        "arv": "http://arvados.org/cwl#"
+      },
       "class": "Workflow",
-      "cwlVersion": "v1.2.0-dev1",
+      "cwlVersion": "v1.0",
       "hints": [],
       "id": "#main",
       "inputs": [
@@ -59,10 +62,10 @@
           "run": {
             "baseCommand": "sleep",
             "class": "CommandLineTool",
-            "id": "#main/sleep1/run/subtool",
+            "id": "#main/sleep1/subtool",
             "inputs": [
               {
-                "id": "#main/sleep1/run/subtool/sleeptime",
+                "id": "#main/sleep1/subtool/sleeptime",
                 "inputBinding": {
                   "position": 1
                 },
@@ -71,7 +74,7 @@
             ],
             "outputs": [
               {
-                "id": "#main/sleep1/run/subtool/out",
+                "id": "#main/sleep1/subtool/out",
                 "outputBinding": {
                   "outputEval": "out"
                 },
@@ -83,5 +86,5 @@
       ]
     }
   ],
-  "cwlVersion": "v1.2.0-dev1"
-}
+  "cwlVersion": "v1.0"
+}
\ No newline at end of file

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