[ARVADOS] updated: 1.2.0-387-g25924379d
Git user
git at public.curoverse.com
Tue Nov 13 22:07:54 EST 2018
Summary of changes:
sdk/cwl/tests/{ => federation/cases}/cat.cwl | 8 ++--
...{twostep-both-remote.cwl => scatter-gather.cwl} | 27 +++++++------
.../{base-case-input.txt => scatter-gather-s1.txt} | 2 +-
.../{base-case-input.txt => scatter-gather-s2.txt} | 2 +-
.../{base-case-input.txt => scatter-gather-s3.txt} | 2 +-
sdk/cwl/tests/federation/main.cwl | 44 ++++++++++++++++++++++
6 files changed, 65 insertions(+), 20 deletions(-)
copy sdk/cwl/tests/{ => federation/cases}/cat.cwl (72%)
copy sdk/cwl/tests/federation/cases/{twostep-both-remote.cwl => scatter-gather.cwl} (54%)
copy sdk/cwl/tests/federation/data/{base-case-input.txt => scatter-gather-s1.txt} (92%)
copy sdk/cwl/tests/federation/data/{base-case-input.txt => scatter-gather-s2.txt} (92%)
copy sdk/cwl/tests/federation/data/{base-case-input.txt => scatter-gather-s3.txt} (92%)
via 25924379d72321d0f2e2bf2a520bbfeb7a14a26a (commit)
from 27486bdd930b28f175a70ff3cfa41ec69aed8be0 (commit)
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commit 25924379d72321d0f2e2bf2a520bbfeb7a14a26a
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Tue Nov 13 22:06:36 2018 -0500
14198: Add scatter-gather
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/federation/cases/cat.cwl b/sdk/cwl/tests/federation/cases/cat.cwl
new file mode 100644
index 000000000..17132fe61
--- /dev/null
+++ b/sdk/cwl/tests/federation/cases/cat.cwl
@@ -0,0 +1,14 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+ inp:
+ type: File[]
+ inputBinding: {}
+outputs:
+ joined: stdout
+stdout: joined.txt
+baseCommand: cat
diff --git a/sdk/cwl/tests/federation/cases/scatter-gather.cwl b/sdk/cwl/tests/federation/cases/scatter-gather.cwl
new file mode 100644
index 000000000..a0519b29d
--- /dev/null
+++ b/sdk/cwl/tests/federation/cases/scatter-gather.cwl
@@ -0,0 +1,34 @@
+# 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:scatter-gather
+ ScatterFeatureRequirement: {}
+inputs:
+ shards: File[]
+ clusters: string[]
+outputs:
+ joined:
+ type: File
+ outputSource: cat/joined
+steps:
+ md5sum:
+ in:
+ inp: shards
+ runOnCluster: clusters
+ scatter: [inp, runOnCluster]
+ scatterMethod: dotproduct
+ out: [hash]
+ run: md5sum.cwl
+ cat:
+ in:
+ inp: md5sum/hash
+ out: [joined]
+ run: cat.cwl
diff --git a/sdk/cwl/tests/federation/data/scatter-gather-s1.txt b/sdk/cwl/tests/federation/data/scatter-gather-s1.txt
new file mode 100644
index 000000000..cc732e3e7
--- /dev/null
+++ b/sdk/cwl/tests/federation/data/scatter-gather-s1.txt
@@ -0,0 +1,16 @@
+Call me scatter-gather-s1. 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/data/scatter-gather-s2.txt b/sdk/cwl/tests/federation/data/scatter-gather-s2.txt
new file mode 100644
index 000000000..3b57ee1ea
--- /dev/null
+++ b/sdk/cwl/tests/federation/data/scatter-gather-s2.txt
@@ -0,0 +1,16 @@
+Call me scatter-gather-s2. 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/data/scatter-gather-s3.txt b/sdk/cwl/tests/federation/data/scatter-gather-s3.txt
new file mode 100644
index 000000000..06f77d285
--- /dev/null
+++ b/sdk/cwl/tests/federation/data/scatter-gather-s3.txt
@@ -0,0 +1,16 @@
+Call me scatter-gather-s3. 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 7e1d878af..9058fde0d 100755
--- a/sdk/cwl/tests/federation/main.cwl
+++ b/sdk/cwl/tests/federation/main.cwl
@@ -369,3 +369,47 @@ steps:
- 2d3a4a840077390a0d7788f169eaba89+112 # runner output json
out: [out, success]
run: framework/testcase.cwl
+
+ scatter-gather:
+ doc: ""
+ 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/scatter-gather.cwl
+ secondaryFiles:
+ - class: File
+ location: cases/md5sum.cwl
+ - class: File
+ location: cases/cat.cwl
+ obj:
+ default:
+ shards:
+ - class: File
+ location: data/scatter-gather-s1.txt
+ - class: File
+ location: data/scatter-gather-s2.txt
+ - class: File
+ location: data/scatter-gather-s3.txt
+ valueFrom: |-
+ ${
+ self["clusters"] = inputs.arvados_cluster_ids;
+ return self;
+ }
+ runner_cluster: { valueFrom: "$(inputs.arvados_cluster_ids[0])" }
+ scrub_image: {default: "arvados/fed-test:scatter-gather"}
+ scrub_collections:
+ default:
+ - 99cc18329bce1b4a5fe6c4cf60477668+209 # input collection
+ - 2e570e844e03c7027baad148642d726f+51 # s1 md5sum output collection
+ - 61c88ee7811d0b849b5c06376eb065a6+51 # s2 md5sum output collection
+ - 85aaf18d638045fe609e025d3a319b2a+51 # s3 md5sum output collection
+ - ec44bcba77e65128f1a8f843d881ede4+56 # cat output collection
+ - 89de265942800ae36549109969940363+117 # runner output json
+ out: [out, success]
+ run: framework/testcase.cwl
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