[ARVADOS] updated: 1.2.0-386-g27486bdd9
Git user
git at public.curoverse.com
Tue Nov 13 17:29:16 EST 2018
Summary of changes:
.../cases/{rev.cwl => rev-input-to-output.cwl} | 15 ++++++--
...-remote.cwl => twostep-remote-copy-to-home.cwl} | 4 +-
...e-input.txt => twostep-remote-copy-to-home.txt} | 2 +-
sdk/cwl/tests/federation/main.cwl | 45 ++++++++++++++++++++++
4 files changed, 59 insertions(+), 7 deletions(-)
copy sdk/cwl/tests/federation/cases/{rev.cwl => rev-input-to-output.cwl} (59%)
copy sdk/cwl/tests/federation/cases/{twostep-both-remote.cwl => twostep-remote-copy-to-home.cwl} (86%)
copy sdk/cwl/tests/federation/data/{runner-remote-step-home-input.txt => twostep-remote-copy-to-home.txt} (91%)
via 27486bdd930b28f175a70ff3cfa41ec69aed8be0 (commit)
from d2f357b4129800a340c834f56fdd1fc534072a20 (commit)
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commit 27486bdd930b28f175a70ff3cfa41ec69aed8be0
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Tue Nov 13 17:28:59 2018 -0500
14198: Add test twostep-remote-copy-to-home
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/federation/cases/rev-input-to-output.cwl b/sdk/cwl/tests/federation/cases/rev-input-to-output.cwl
new file mode 100644
index 000000000..ac9f4e915
--- /dev/null
+++ b/sdk/cwl/tests/federation/cases/rev-input-to-output.cwl
@@ -0,0 +1,30 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.0
+class: CommandLineTool
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+requirements:
+ InlineJavascriptRequirement: {}
+ arv:ClusterTarget:
+ cluster_id: $(inputs.runOnCluster)
+ ShellCommandRequirement: {}
+inputs:
+ inp:
+ type: File
+ runOnCluster: string
+outputs:
+ original:
+ type: File
+ outputBinding:
+ glob: $(inputs.inp.basename)
+ revhash:
+ type: stdout
+stdout: rev-$(inputs.inp.basename)
+arguments:
+ - shellQuote: false
+ valueFrom: |
+ ln -s $(inputs.inp.path) $(inputs.inp.basename) &&
+ rev $(inputs.inp.basename)
diff --git a/sdk/cwl/tests/federation/cases/twostep-remote-copy-to-home.cwl b/sdk/cwl/tests/federation/cases/twostep-remote-copy-to-home.cwl
new file mode 100644
index 000000000..d1f5896f3
--- /dev/null
+++ b/sdk/cwl/tests/federation/cases/twostep-remote-copy-to-home.cwl
@@ -0,0 +1,35 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.0
+class: Workflow
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+requirements:
+ InlineJavascriptRequirement: {}
+ DockerRequirement:
+ dockerPull: arvados/fed-test:twostep-remote-copy-to-home
+inputs:
+ inp:
+ type: File
+ inputBinding: {}
+ md5sumCluster: string
+ revCluster: string
+outputs:
+ hash:
+ type: File
+ outputSource: md5sum/hash
+steps:
+ md5sum:
+ in:
+ inp: inp
+ runOnCluster: md5sumCluster
+ out: [hash]
+ run: md5sum.cwl
+ rev:
+ in:
+ inp: md5sum/hash
+ runOnCluster: revCluster
+ out: [revhash]
+ run: rev-input-to-output.cwl
diff --git a/sdk/cwl/tests/federation/data/twostep-remote-copy-to-home.txt b/sdk/cwl/tests/federation/data/twostep-remote-copy-to-home.txt
new file mode 100644
index 000000000..c0f72ef1f
--- /dev/null
+++ b/sdk/cwl/tests/federation/data/twostep-remote-copy-to-home.txt
@@ -0,0 +1,16 @@
+Call me twostep-remote-copy-to-home. Some years ago--never mind how long precisely--having
+little or no money in my purse, and nothing particular to interest me on
+shore, I thought I would sail about a little and see the watery part of
+the world. It is a way I have of driving off the spleen and regulating
+the circulation. Whenever I find myself growing grim about the mouth;
+whenever it is a damp, drizzly November in my soul; whenever I find
+myself involuntarily pausing before coffin warehouses, and bringing up
+the rear of every funeral I meet; and especially whenever my hypos get
+such an upper hand of me, that it requires a strong moral principle to
+prevent me from deliberately stepping into the street, and methodically
+knocking people's hats off--then, I account it high time to get to sea
+as soon as I can. This is my substitute for pistol and ball. With a
+philosophical flourish Cato throws himself upon his sword; I quietly
+take to the ship. There is nothing surprising in this. If they but knew
+it, almost all men in their degree, some time or other, cherish very
+nearly the same feelings towards the ocean with me.
diff --git a/sdk/cwl/tests/federation/main.cwl b/sdk/cwl/tests/federation/main.cwl
index 2a6b61a3e..7e1d878af 100755
--- a/sdk/cwl/tests/federation/main.cwl
+++ b/sdk/cwl/tests/federation/main.cwl
@@ -324,3 +324,48 @@ steps:
- ddfa58a81953dad08436d571615dd584+112 # runner output json
out: [out, success]
run: framework/testcase.cwl
+
+ twostep-remote-copy-to-home:
+ doc: |
+ Two step workflow. The runner is on the home cluster, the first
+ step is on the remote cluster, the second step is on the home
+ cluster, and propagates its input file directly from input to
+ output by symlinking the input file in the output directory.
+ Tests that crunch-run will copy blocks from remote to local
+ when preparing output collection.
+ in:
+ arvados_api_token: arvados_api_token
+ arvado_api_host_insecure: arvado_api_host_insecure
+ arvados_api_hosts: arvados_api_hosts
+ arvados_cluster_ids: arvados_cluster_ids
+ acr: acr
+ wf:
+ default:
+ class: File
+ location: cases/twostep-remote-copy-to-home.cwl
+ secondaryFiles:
+ - class: File
+ location: cases/md5sum.cwl
+ - class: File
+ location: cases/rev-input-to-output.cwl
+ obj:
+ default:
+ inp:
+ class: File
+ location: data/twostep-remote-copy-to-home.txt
+ valueFrom: |-
+ ${
+ self["md5sumCluster"] = inputs.arvados_cluster_ids[1];
+ self["revCluster"] = inputs.arvados_cluster_ids[0];
+ return self;
+ }
+ runner_cluster: { valueFrom: "$(inputs.arvados_cluster_ids[0])" }
+ scrub_image: {default: "arvados/fed-test:twostep-remote-copy-to-home"}
+ scrub_collections:
+ default:
+ - 538887bc29a3098bf79abdb8536d17bd+79 # input collection
+ - 14da0e0d52d7ab2945427074b275e9ee+51 # md5sum output collection
+ - 2d3a4a840077390a0d7788f169eaba89+112 # rev output collection
+ - 2d3a4a840077390a0d7788f169eaba89+112 # runner output json
+ out: [out, success]
+ run: framework/testcase.cwl
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