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@curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index ba60333648eabdb4d308503b3e8ac20b88ad34e1..ddd3c00764c7b0fb42fe97adf50622bd1b23e9cb 100644 (file)
--- 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 2239e0f9df952b9ab75a7e9a96ab46953ab29f94..f0be83032415bf64e0a64c793c8b0b7e9974bdd3 100644 (file)
--- 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 5a359d22cda67be2e5bc1212e8536acb49a8f825..95730a69b11199bff6f20f7051ab91141d9c1acd 100644 (file)
--- 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 8677db92a062df3bc954b5f3caf98cbd73172eef..d331e3552d8210aafeed636c43530114288a4239 100644 (file)
--- 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 035c1e97e0499649f6f7e4993e99f7ba566f6a50..c54e1707ff0ef7fdb741305ff6804bb19cfdbaac 100644 (file)
--- 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