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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 2239e0f9df952b9ab75a7e9a96ab46953ab29f94..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
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
import arvados_cwl.arvdocker
from .pathmapper import ArvPathMapper, trim_listing, collection_pdh_pattern, collection_uuid_pattern
@@
-392,7
+393,7
@@
def upload_dependencies(arvrunner, name, document_loader,
discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
if "$schemas" in workflowobj:
discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
if "$schemas" in workflowobj:
- sch =
[]
+ sch =
CommentedSeq()
for s in workflowobj["$schemas"]:
sch.append(mapper.mapper(s).resolved)
workflowobj["$schemas"] = sch
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 = {}
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)}
rewrite_to_orig = {v: k for k,v in viewitems(rewrites)}