16482: bump a-c-r's cwltool dependency to version 3.0.20200530110633 so

[arvados.git] / sdk / cwl / arvados_cwl / runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 4ca010bab1dbba1c8b9f135c228492e4d0ab7dcf..7bb66a158e50646f1fc984df7ea30ccd31528bf3 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -42,6 +42,7 @@ import schema_salad.validate as validate
 import arvados.collection
 from .util import collectionUUID
 import ruamel.yaml as yaml
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 import arvados_cwl.arvdocker
 from .pathmapper import ArvPathMapper, trim_listing, collection_pdh_pattern, collection_uuid_pattern
@@ -334,7 +335,7 @@ def upload_dependencies(arvrunner, name, document_loader,
                                  builder_job_order,
                                  discovered)
 
-    copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri)
+    copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri, checklinks=False)
     visit_class(copied, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
 
     for d in list(discovered):
@@ -392,7 +393,7 @@ def upload_dependencies(arvrunner, name, document_loader,
             discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
 
     if "$schemas" in workflowobj:
-        sch = []
+        sch = CommentedSeq()
         for s in workflowobj["$schemas"]:
             sch.append(mapper.mapper(s).resolved)
         workflowobj["$schemas"] = sch
@@ -424,8 +425,9 @@ 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)}
 
@@ -578,7 +580,8 @@ class Runner(Process):
     """Base class for runner processes, which submit an instance of
     arvados-cwl-runner and wait for the final result."""
 
-    def __init__(self, runner, tool, loadingContext, enable_reuse,
+    def __init__(self, runner, updated_tool,
+                 tool, loadingContext, enable_reuse,
                  output_name, output_tags, submit_runner_ram=0,
                  name=None, on_error=None, submit_runner_image=None,
                  intermediate_output_ttl=0, merged_map=None,
@@ -587,10 +590,9 @@ class Runner(Process):
                  collection_cache_is_default=True):
 
         loadingContext = loadingContext.copy()
-        loadingContext.metadata = loadingContext.metadata.copy()
-        loadingContext.metadata["cwlVersion"] = INTERNAL_VERSION
+        loadingContext.metadata = updated_tool.metadata.copy()
 
-        super(Runner, self).__init__(tool.tool, loadingContext)
+        super(Runner, self).__init__(updated_tool.tool, loadingContext)
 
         self.arvrunner = runner
         self.embedded_tool = tool