Error if colon in input/output paths when running with DockerRequirement

[mccalluc]

Expected Behavior

When run with DockerRequirement, input paths with colons should work.

Actual Behavior

It fails:

INFO [job workflow.cwl] /tmp/4cf898fg$ docker \
   run \
   -i \
   --volume=/tmp/4cf898fg:/HZfoyx:rw \
   --volume=/tmp/e8pu8i7i:/tmp:rw \
   --volume=/home/airflow/repositories/ingest-pipeline/src/ingest-pipeline/airflow/data/temp/trig_
_2020-02-08T22:34:44.290910+00:00/cwl_out/cluster-marker-genes:/var/lib/cwl/stg706d994b-d3e7-49fd-9
9a2-d236a8783326/cluster-marker-genes:ro \
   --workdir=/HZfoyx \
   --read-only=true \
   --user=1008:1008 \
...
docker: Error response from daemon: invalid volume specification: '/home/airflow/repositories/inges
t-pipeline/src/ingest-pipeline/airflow/data/temp/trig__2020-02-08T22:34:44.290910+00:00/cwl_out/clu
ster-marker-genes:/var/lib/cwl/stg706d994b-d3e7-49fd-99a2-d236a8783326/cluster-marker-genes:ro'.

(from hubmapconsortium/airflow-dev#33)

Root Cause

in cwltool/docker.py:

    def append_volume(runtime, source, target, writable=False):
        # type: (List[str], str, str, bool) -> None
        """Add binding arguments to the runtime list."""
        runtime.append(
            "--volume={}:{}:{}".format(
                docker_windows_path_adjust(source), target, "rw" if writable else "ro"
            )
        )

With the --volume, colons have a special meaning. The solution is to use --mount instead.

Next Steps

I'll make a PR to address this.

Workflow Code

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Full Traceback

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Your Environment

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