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19385: Clean up debug prints
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
arvcontainer.py
diff --git
a/sdk/cwl/arvados_cwl/arvcontainer.py
b/sdk/cwl/arvados_cwl/arvcontainer.py
index a15c085da775f9eb0a36331d2cbcd23e84e888fe..742906c616514b9bcd2317cfeb4a11697f1c8522 100644
(file)
--- a/
sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/
sdk/cwl/arvados_cwl/arvcontainer.py
@@
-17,7
+17,7
@@
import uuid
import math
import arvados_cwl.util
import math
import arvados_cwl.util
-import ruamel.yaml
as yaml
+import ruamel.yaml
from cwltool.errors import WorkflowException
from cwltool.process import UnsupportedRequirement, shortname
from cwltool.errors import WorkflowException
from cwltool.process import UnsupportedRequirement, shortname
@@
-250,11
+250,7
@@
class ArvadosContainer(JobBase):
container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
docker_req,
runtimeContext.pull_image,
container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
docker_req,
runtimeContext.pull_image,
- runtimeContext.project_uuid,
- runtimeContext.force_docker_pull,
- runtimeContext.tmp_outdir_prefix,
- runtimeContext.match_local_docker,
- runtimeContext.copy_deps)
+ runtimeContext)
network_req, _ = self.get_requirement("NetworkAccess")
if network_req:
network_req, _ = self.get_requirement("NetworkAccess")
if network_req:
@@
-536,20
+532,24
@@
class RunnerContainer(Runner):
"portable_data_hash": "%s" % workflowcollection
}
elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
"portable_data_hash": "%s" % workflowcollection
}
elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
- workflowpath = "/var/lib/cwl/workflow.json#main"
- record = self.arvrunner.api.workflows().get(uuid=self.embedded_tool.tool["id"][6:33]).execute(num_retries=self.arvrunner.num_retries)
- packed = yaml.safe_load(record["definition"])
+ uuid, frg = urllib.parse.urldefrag(self.embedded_tool.tool["id"])
+ workflowpath = "/var/lib/cwl/workflow.json#" + frg
+ packedtxt = self.loadingContext.loader.fetch_text(uuid)
+ yaml = ruamel.yaml.YAML(typ='safe', pure=True)
+ packed = yaml.load(packedtxt)
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
"content": packed
}
container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
else:
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
"content": packed
}
container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
else:
- packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext, git_info)
+ main = self.loadingContext.loader.idx["_:main"]
+ if main.get("id") == "_:main":
+ del main["id"]
workflowpath = "/var/lib/cwl/workflow.json#main"
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
workflowpath = "/var/lib/cwl/workflow.json#main"
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
- "content":
packed
+ "content":
main
}
container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
}
container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
@@
-622,6
+622,9
@@
class RunnerContainer(Runner):
if runtimeContext.prefer_cached_downloads:
command.append("--prefer-cached-downloads")
if runtimeContext.prefer_cached_downloads:
command.append("--prefer-cached-downloads")
+ if self.fast_parser:
+ command.append("--fast-parser")
+
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command