10081: Custom extension of v1.0 schema to recognize RunInSingleContainer.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 1256260598c3e5c29bbca02e8de752698ee2cbfd..20bbc41bd32627d020f156c4b4e86ac31663971b 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -15,6 +15,7 @@ import pkg_resources  # part of setuptools
 from cwltool.errors import WorkflowException
 import cwltool.main
 import cwltool.workflow
+import schema_salad
 
 import arvados
 import arvados.config
@@ -364,6 +365,15 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     return parser
 
+def add_arv_hints():
+    cache = {}
+    res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
+    cache["https://w3id.org/cwl/arv-cwl-schema.yml"] = res.read()
+    res.close()
+    _, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
+    _, extnames, _, _ = schema_salad.schema.load_schema("https://w3id.org/cwl/arv-cwl-schema.yml", cache=cache)
+    for n in extnames.names:
+        cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
 
 def main(args, stdout, stderr, api_client=None):
     parser = arg_parser()
@@ -373,6 +383,8 @@ def main(args, stdout, stderr, api_client=None):
     if (arvargs.create_template or arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
         job_order_object = ({}, "")
 
+    add_arv_hints()
+
     try:
         if api_client is None:
             api_client=arvados.api('v1', model=OrderedJsonModel())

diff --git a/sdk/cwl/arvados_cwl/arv-cwl-schema.yml b/sdk/cwl/arvados_cwl/arv-cwl-schema.yml
new file mode 100644 (file)
index 0000000..2e5044d
--- /dev/null
+++ b/sdk/cwl/arvados_cwl/arv-cwl-schema.yml
@@ -0,0 +1,14 @@
+$base: "http://arvados.org/cwl#"
+$graph:
+- name: RunInSingleContainer
+  type: record
+  doc: |
+    Indicates that a subworkflow should run in a single container
+    and not be scheduled as separate steps.
+  fields:
+    - name: class
+      type: string
+      doc: "Always 'arv:RunInSingleContainer'"
+      jsonldPredicate:
+        _id: "@type"
+        _type: "@vocab"

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index a6e4c5e294750b5ff508b239c0668ce372302f03..b55874477114767b0a38d086cece60b697aa48ed 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -25,6 +25,7 @@ setup(name='arvados-cwl-runner',
       download_url="https://github.com/curoverse/arvados.git",
       license='Apache 2.0',
       packages=find_packages(),
+      package_data={'arvados_cwl': ['arv-cwl-schema.yml']},
       scripts=[
           'bin/cwl-runner',
           'bin/arvados-cwl-runner'