[ARVADOS] updated: 1.2.0-328-g001bb1141
Git user
git at public.curoverse.com
Thu Nov 8 22:09:02 EST 2018
Summary of changes:
.licenseignore | 2 +-
.../federation/{ => arvbox}/arvbox-fed-config.cwl | 0
.../tests/federation/{ => arvbox}/arvbox-fed.cwl | 0
sdk/cwl/tests/federation/arvbox/arvbox-main.cwl | 38 ++++++++++
.../tests/federation/{ => arvbox}/arvbox-mkdir.cwl | 0
.../federation/{ => arvbox}/arvbox-setup-user.cwl | 0
.../tests/federation/{ => arvbox}/arvbox-start.cwl | 0
.../tests/federation/{ => arvbox}/arvbox-stop.cwl | 0
.../federation/{md5sum.cwl => cases/base-case.cwl} | 19 ++---
sdk/cwl/tests/federation/{ => cases}/md5sum.cwl | 13 +---
.../runner-home-step-remote.cwl} | 19 ++---
.../runner-remote-step-home.cwl} | 19 ++---
.../{whale.txt => data/base-case-input.txt} | 2 +-
.../runner-home-step-remote-input.txt} | 2 +-
.../runner-remote-step-home-input.txt} | 2 +-
.../{prepare.cwl => framework/check-exist.cwl} | 20 ++----
sdk/cwl/tests/federation/framework/check_exist.py | 25 +++++++
sdk/cwl/tests/federation/framework/dockerbuild.cwl | 21 ++++++
.../tests/federation/{ => framework}/prepare.cwl | 4 +-
.../tests/federation/{ => framework}/prepare.py | 0
.../tests/federation/{ => framework}/run-acr.cwl | 3 +-
.../tests/federation/{ => framework}/setup_user.py | 0
.../tests/federation/{ => framework}/testcase.cwl | 22 +++++-
sdk/cwl/tests/federation/main.cwl | 84 ++++++++++++++++------
24 files changed, 213 insertions(+), 82 deletions(-)
rename sdk/cwl/tests/federation/{ => arvbox}/arvbox-fed-config.cwl (100%)
rename sdk/cwl/tests/federation/{ => arvbox}/arvbox-fed.cwl (100%)
create mode 100644 sdk/cwl/tests/federation/arvbox/arvbox-main.cwl
rename sdk/cwl/tests/federation/{ => arvbox}/arvbox-mkdir.cwl (100%)
rename sdk/cwl/tests/federation/{ => arvbox}/arvbox-setup-user.cwl (100%)
rename sdk/cwl/tests/federation/{ => arvbox}/arvbox-start.cwl (100%)
rename sdk/cwl/tests/federation/{ => arvbox}/arvbox-stop.cwl (100%)
copy sdk/cwl/tests/federation/{md5sum.cwl => cases/base-case.cwl} (63%)
copy sdk/cwl/tests/federation/{ => cases}/md5sum.cwl (55%)
copy sdk/cwl/tests/federation/{md5sum.cwl => cases/runner-home-step-remote.cwl} (63%)
rename sdk/cwl/tests/federation/{md5sum.cwl => cases/runner-remote-step-home.cwl} (63%)
copy sdk/cwl/tests/federation/{whale.txt => data/base-case-input.txt} (93%)
copy sdk/cwl/tests/federation/{whale.txt => data/runner-home-step-remote-input.txt} (92%)
rename sdk/cwl/tests/federation/{whale.txt => data/runner-remote-step-home-input.txt} (92%)
copy sdk/cwl/tests/federation/{prepare.cwl => framework/check-exist.cwl} (65%)
create mode 100644 sdk/cwl/tests/federation/framework/check_exist.py
create mode 100644 sdk/cwl/tests/federation/framework/dockerbuild.cwl
rename sdk/cwl/tests/federation/{ => framework}/prepare.cwl (92%)
rename sdk/cwl/tests/federation/{ => framework}/prepare.py (100%)
rename sdk/cwl/tests/federation/{ => framework}/run-acr.cwl (91%)
rename sdk/cwl/tests/federation/{ => framework}/setup_user.py (100%)
rename sdk/cwl/tests/federation/{ => framework}/testcase.cwl (71%)
via 001bb11415036a72fb19d97f5ef933685b0e4451 (commit)
from 457672f2662d6c726cd0c66ef5a8d08ebe9791eb (commit)
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not appeared on any other notification email; so we list those
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commit 001bb11415036a72fb19d97f5ef933685b0e4451
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Thu Nov 8 16:13:18 2018 -0500
14198: Refactored. Tests use isolated inputs. Return success boolean
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/.licenseignore b/.licenseignore
index 5d3eff344..113bf4fa4 100644
--- a/.licenseignore
+++ b/.licenseignore
@@ -46,7 +46,7 @@ docker/jobs/apt.arvados.org.list
*/script/rails
sdk/cwl/tests/input/blorp.txt
sdk/cwl/tests/tool/blub.txt
-sdk/cwl/tests/federation/whale.txt
+sdk/cwl/tests/federation/data/*
sdk/go/manifest/testdata/*_manifest
sdk/java/.classpath
sdk/java/pom.xml
diff --git a/sdk/cwl/tests/federation/arvbox-fed-config.cwl b/sdk/cwl/tests/federation/arvbox/arvbox-fed-config.cwl
similarity index 100%
rename from sdk/cwl/tests/federation/arvbox-fed-config.cwl
rename to sdk/cwl/tests/federation/arvbox/arvbox-fed-config.cwl
diff --git a/sdk/cwl/tests/federation/arvbox-fed.cwl b/sdk/cwl/tests/federation/arvbox/arvbox-fed.cwl
similarity index 100%
rename from sdk/cwl/tests/federation/arvbox-fed.cwl
rename to sdk/cwl/tests/federation/arvbox/arvbox-fed.cwl
diff --git a/sdk/cwl/tests/federation/arvbox/arvbox-main.cwl b/sdk/cwl/tests/federation/arvbox/arvbox-main.cwl
new file mode 100644
index 000000000..a6fd00823
--- /dev/null
+++ b/sdk/cwl/tests/federation/arvbox/arvbox-main.cwl
@@ -0,0 +1,38 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.0
+class: Workflow
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+requirements:
+ cwltool:LoadListingRequirement:
+ loadListing: no_listing
+ SubworkflowFeatureRequirement: {}
+inputs:
+ arvbox_base: Directory
+ acr: string?
+outputs: []
+steps:
+ run-arvbox:
+ in:
+ containers:
+ default: [fedbox1, fedbox2, fedbox3]
+ arvbox_base: arvbox_base
+ out: [cluster_ids, container_hosts, test_user_uuid, test_user_token]
+ run: arvbox-fed.cwl
+ run-main:
+ in:
+ arvados_api_host_home: {source: run-arvbox/container_hosts, valueFrom: "$(self[0])"}
+ arvados_home_id: {source: run-arvbox/cluster_ids, valueFrom: "$(self[0])"}
+ arvados_api_token: run-arvbox/test_user_token
+ arvado_api_host_insecure: {default: true}
+ arvados_api_host_clusterB: {source: run-arvbox/container_hosts, valueFrom: "$(self[1])"}
+ arvados_clusterB_id: {source: run-arvbox/cluster_ids, valueFrom: "$(self[1])"}
+ arvados_api_host_clusterC: {source: run-arvbox/container_hosts, valueFrom: "$(self[2])"}
+ arvados_clusterC_id: {source: run-arvbox/cluster_ids, valueFrom: "$(self[2])"}
+ acr: acr
+ out: [base-case-out, runner-home-step-remote-out]
+ run: main.cwl
diff --git a/sdk/cwl/tests/federation/arvbox-mkdir.cwl b/sdk/cwl/tests/federation/arvbox/arvbox-mkdir.cwl
similarity index 100%
rename from sdk/cwl/tests/federation/arvbox-mkdir.cwl
rename to sdk/cwl/tests/federation/arvbox/arvbox-mkdir.cwl
diff --git a/sdk/cwl/tests/federation/arvbox-setup-user.cwl b/sdk/cwl/tests/federation/arvbox/arvbox-setup-user.cwl
similarity index 100%
rename from sdk/cwl/tests/federation/arvbox-setup-user.cwl
rename to sdk/cwl/tests/federation/arvbox/arvbox-setup-user.cwl
diff --git a/sdk/cwl/tests/federation/arvbox-start.cwl b/sdk/cwl/tests/federation/arvbox/arvbox-start.cwl
similarity index 100%
rename from sdk/cwl/tests/federation/arvbox-start.cwl
rename to sdk/cwl/tests/federation/arvbox/arvbox-start.cwl
diff --git a/sdk/cwl/tests/federation/arvbox-stop.cwl b/sdk/cwl/tests/federation/arvbox/arvbox-stop.cwl
similarity index 100%
rename from sdk/cwl/tests/federation/arvbox-stop.cwl
rename to sdk/cwl/tests/federation/arvbox/arvbox-stop.cwl
diff --git a/sdk/cwl/tests/federation/md5sum.cwl b/sdk/cwl/tests/federation/cases/base-case.cwl
similarity index 63%
copy from sdk/cwl/tests/federation/md5sum.cwl
copy to sdk/cwl/tests/federation/cases/base-case.cwl
index 18f3fb0f9..2e0ff64c6 100644
--- a/sdk/cwl/tests/federation/md5sum.cwl
+++ b/sdk/cwl/tests/federation/cases/base-case.cwl
@@ -3,13 +3,13 @@
# SPDX-License-Identifier: Apache-2.0
cwlVersion: v1.0
-class: CommandLineTool
+class: Workflow
$namespaces:
arv: "http://arvados.org/cwl#"
requirements:
InlineJavascriptRequirement: {}
DockerRequirement:
- dockerPull: debian:9
+ dockerPull: arvados/fed-test:base-case
arv:ClusterTarget:
cluster_id: $(inputs.runOnCluster)
inputs:
@@ -19,10 +19,11 @@ inputs:
runOnCluster: string
outputs:
hash:
- type: string
- outputBinding:
- glob: out.txt
- loadContents: true
- outputEval: $(self[0].contents.substr(0, 32))
-stdout: out.txt
-baseCommand: md5sum
+ type: File
+ outputSource: md5sum/hash
+steps:
+ md5sum:
+ in:
+ inp: inp
+ out: [hash]
+ run: md5sum.cwl
\ No newline at end of file
diff --git a/sdk/cwl/tests/federation/md5sum.cwl b/sdk/cwl/tests/federation/cases/md5sum.cwl
similarity index 55%
copy from sdk/cwl/tests/federation/md5sum.cwl
copy to sdk/cwl/tests/federation/cases/md5sum.cwl
index 18f3fb0f9..af119990a 100644
--- a/sdk/cwl/tests/federation/md5sum.cwl
+++ b/sdk/cwl/tests/federation/cases/md5sum.cwl
@@ -8,21 +8,14 @@ $namespaces:
arv: "http://arvados.org/cwl#"
requirements:
InlineJavascriptRequirement: {}
- DockerRequirement:
- dockerPull: debian:9
- arv:ClusterTarget:
- cluster_id: $(inputs.runOnCluster)
inputs:
inp:
type: File
- inputBinding: {}
- runOnCluster: string
outputs:
hash:
- type: string
+ type: File
outputBinding:
glob: out.txt
- loadContents: true
- outputEval: $(self[0].contents.substr(0, 32))
+stdin: $(inputs.inp.path)
stdout: out.txt
-baseCommand: md5sum
+arguments: ["md5sum", "-"]
diff --git a/sdk/cwl/tests/federation/md5sum.cwl b/sdk/cwl/tests/federation/cases/runner-home-step-remote.cwl
similarity index 63%
copy from sdk/cwl/tests/federation/md5sum.cwl
copy to sdk/cwl/tests/federation/cases/runner-home-step-remote.cwl
index 18f3fb0f9..70d017639 100644
--- a/sdk/cwl/tests/federation/md5sum.cwl
+++ b/sdk/cwl/tests/federation/cases/runner-home-step-remote.cwl
@@ -3,13 +3,13 @@
# SPDX-License-Identifier: Apache-2.0
cwlVersion: v1.0
-class: CommandLineTool
+class: Workflow
$namespaces:
arv: "http://arvados.org/cwl#"
requirements:
InlineJavascriptRequirement: {}
DockerRequirement:
- dockerPull: debian:9
+ dockerPull: arvados/fed-test:runner-home-step-remote
arv:ClusterTarget:
cluster_id: $(inputs.runOnCluster)
inputs:
@@ -19,10 +19,11 @@ inputs:
runOnCluster: string
outputs:
hash:
- type: string
- outputBinding:
- glob: out.txt
- loadContents: true
- outputEval: $(self[0].contents.substr(0, 32))
-stdout: out.txt
-baseCommand: md5sum
+ type: File
+ outputSource: md5sum/hash
+steps:
+ md5sum:
+ in:
+ inp: inp
+ out: [hash]
+ run: md5sum.cwl
\ No newline at end of file
diff --git a/sdk/cwl/tests/federation/md5sum.cwl b/sdk/cwl/tests/federation/cases/runner-remote-step-home.cwl
similarity index 63%
rename from sdk/cwl/tests/federation/md5sum.cwl
rename to sdk/cwl/tests/federation/cases/runner-remote-step-home.cwl
index 18f3fb0f9..33681f18e 100644
--- a/sdk/cwl/tests/federation/md5sum.cwl
+++ b/sdk/cwl/tests/federation/cases/runner-remote-step-home.cwl
@@ -3,13 +3,13 @@
# SPDX-License-Identifier: Apache-2.0
cwlVersion: v1.0
-class: CommandLineTool
+class: Workflow
$namespaces:
arv: "http://arvados.org/cwl#"
requirements:
InlineJavascriptRequirement: {}
DockerRequirement:
- dockerPull: debian:9
+ dockerPull: arvados/fed-test:runner-remote-step-home
arv:ClusterTarget:
cluster_id: $(inputs.runOnCluster)
inputs:
@@ -19,10 +19,11 @@ inputs:
runOnCluster: string
outputs:
hash:
- type: string
- outputBinding:
- glob: out.txt
- loadContents: true
- outputEval: $(self[0].contents.substr(0, 32))
-stdout: out.txt
-baseCommand: md5sum
+ type: File
+ outputSource: md5sum/hash
+steps:
+ md5sum:
+ in:
+ inp: inp
+ out: [hash]
+ run: md5sum.cwl
\ No newline at end of file
diff --git a/sdk/cwl/tests/federation/whale.txt b/sdk/cwl/tests/federation/data/base-case-input.txt
similarity index 93%
copy from sdk/cwl/tests/federation/whale.txt
copy to sdk/cwl/tests/federation/data/base-case-input.txt
index 425d1ed02..761b840cd 100644
--- a/sdk/cwl/tests/federation/whale.txt
+++ b/sdk/cwl/tests/federation/data/base-case-input.txt
@@ -1,4 +1,4 @@
-Call me Ishmael. Some years ago--never mind how long precisely--having
+Call me base-case. 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
diff --git a/sdk/cwl/tests/federation/whale.txt b/sdk/cwl/tests/federation/data/runner-home-step-remote-input.txt
similarity index 92%
copy from sdk/cwl/tests/federation/whale.txt
copy to sdk/cwl/tests/federation/data/runner-home-step-remote-input.txt
index 425d1ed02..91ab77d12 100644
--- a/sdk/cwl/tests/federation/whale.txt
+++ b/sdk/cwl/tests/federation/data/runner-home-step-remote-input.txt
@@ -1,4 +1,4 @@
-Call me Ishmael. Some years ago--never mind how long precisely--having
+Call me runner-home-step-remote. 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
diff --git a/sdk/cwl/tests/federation/whale.txt b/sdk/cwl/tests/federation/data/runner-remote-step-home-input.txt
similarity index 92%
rename from sdk/cwl/tests/federation/whale.txt
rename to sdk/cwl/tests/federation/data/runner-remote-step-home-input.txt
index 425d1ed02..e5673b848 100644
--- a/sdk/cwl/tests/federation/whale.txt
+++ b/sdk/cwl/tests/federation/data/runner-remote-step-home-input.txt
@@ -1,4 +1,4 @@
-Call me Ishmael. Some years ago--never mind how long precisely--having
+Call me runner-remote-step-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
diff --git a/sdk/cwl/tests/federation/prepare.cwl b/sdk/cwl/tests/federation/framework/check-exist.cwl
similarity index 65%
copy from sdk/cwl/tests/federation/prepare.cwl
copy to sdk/cwl/tests/federation/framework/check-exist.cwl
index 6c82605bb..ebb0fb220 100644
--- a/sdk/cwl/tests/federation/prepare.cwl
+++ b/sdk/cwl/tests/federation/framework/check-exist.cwl
@@ -7,15 +7,11 @@ class: CommandLineTool
requirements:
InitialWorkDirRequirement:
listing:
- - entryname: input.json
- entry: $(JSON.stringify(inputs.obj))
- entryname: config.json
entry: |-
${
return JSON.stringify({
- arvados_cluster_ids: inputs.arvados_cluster_ids,
- scrub_images: inputs.scrub_images,
- scrub_collections: inputs.scrub_collections
+ check_collections: inputs.check_collections
});
}
EnvVarRequirement:
@@ -28,21 +24,19 @@ inputs:
arvados_api_token: string
arvado_api_host_insecure: boolean
arvados_api_host: string
- arvados_cluster_ids: string[]
- wf: File
- obj: Any
- scrub_images: string[]
- scrub_collections: string[]
+ check_collections: string[]
preparescript:
type: File
default:
class: File
- location: prepare.py
+ location: check_exist.py
inputBinding:
position: 1
outputs:
- done:
+ success:
type: boolean
outputBinding:
- outputEval: $(true)
+ glob: success
+ loadContents: true
+ outputEval: $(self[0].contents=="true")
baseCommand: python2
\ No newline at end of file
diff --git a/sdk/cwl/tests/federation/framework/check_exist.py b/sdk/cwl/tests/federation/framework/check_exist.py
new file mode 100644
index 000000000..b3338939e
--- /dev/null
+++ b/sdk/cwl/tests/federation/framework/check_exist.py
@@ -0,0 +1,25 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+import arvados
+import json
+
+api = arvados.api()
+
+with open("config.json") as f:
+ config = json.load(f)
+
+success = True
+for c in config["check_collections"]:
+ try:
+ api.collections().get(uuid=c).execute()
+ except Exception as e:
+ print("Checking for %s got exception %s" % (c, e))
+ success = False
+
+with open("success", "w") as f:
+ if success:
+ f.write("true")
+ else:
+ f.write("false")
diff --git a/sdk/cwl/tests/federation/framework/dockerbuild.cwl b/sdk/cwl/tests/federation/framework/dockerbuild.cwl
new file mode 100644
index 000000000..d00b3e2a5
--- /dev/null
+++ b/sdk/cwl/tests/federation/framework/dockerbuild.cwl
@@ -0,0 +1,21 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+ testcase: string
+outputs:
+ imagename:
+ type: string
+ outputBinding:
+ outputEval: $(inputs.testcase)
+requirements:
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: Dockerfile
+ entry: |-
+ FROM debian at sha256:0a5fcee6f52d5170f557ee2447d7a10a5bdcf715dd7f0250be0b678c556a501b
+ LABEL org.arvados.testcase="$(inputs.testcase)"
+arguments: [docker, build, -t, $(inputs.testcase), "."]
diff --git a/sdk/cwl/tests/federation/prepare.cwl b/sdk/cwl/tests/federation/framework/prepare.cwl
similarity index 92%
rename from sdk/cwl/tests/federation/prepare.cwl
rename to sdk/cwl/tests/federation/framework/prepare.cwl
index 6c82605bb..03f792c5e 100644
--- a/sdk/cwl/tests/federation/prepare.cwl
+++ b/sdk/cwl/tests/federation/framework/prepare.cwl
@@ -14,7 +14,7 @@ requirements:
${
return JSON.stringify({
arvados_cluster_ids: inputs.arvados_cluster_ids,
- scrub_images: inputs.scrub_images,
+ scrub_images: [inputs.scrub_image],
scrub_collections: inputs.scrub_collections
});
}
@@ -31,7 +31,7 @@ inputs:
arvados_cluster_ids: string[]
wf: File
obj: Any
- scrub_images: string[]
+ scrub_image: string
scrub_collections: string[]
preparescript:
type: File
diff --git a/sdk/cwl/tests/federation/prepare.py b/sdk/cwl/tests/federation/framework/prepare.py
similarity index 100%
rename from sdk/cwl/tests/federation/prepare.py
rename to sdk/cwl/tests/federation/framework/prepare.py
diff --git a/sdk/cwl/tests/federation/run-acr.cwl b/sdk/cwl/tests/federation/framework/run-acr.cwl
similarity index 91%
rename from sdk/cwl/tests/federation/run-acr.cwl
rename to sdk/cwl/tests/federation/framework/run-acr.cwl
index 081186506..b720eaa12 100644
--- a/sdk/cwl/tests/federation/run-acr.cwl
+++ b/sdk/cwl/tests/federation/framework/run-acr.cwl
@@ -42,7 +42,8 @@ outputs:
outputBinding:
glob: output.json
loadContents: true
- outputEval: $(JSON.parse(self[0].contents))
+ #outputEval: $(JSON.parse(self[0].contents))
+ outputEval: $(self[0].contents)
stdout: output.json
arguments:
- valueFrom: --disable-reuse
diff --git a/sdk/cwl/tests/federation/setup_user.py b/sdk/cwl/tests/federation/framework/setup_user.py
similarity index 100%
rename from sdk/cwl/tests/federation/setup_user.py
rename to sdk/cwl/tests/federation/framework/setup_user.py
diff --git a/sdk/cwl/tests/federation/testcase.cwl b/sdk/cwl/tests/federation/framework/testcase.cwl
similarity index 71%
rename from sdk/cwl/tests/federation/testcase.cwl
rename to sdk/cwl/tests/federation/framework/testcase.cwl
index b5ef43091..89aa3f98b 100644
--- a/sdk/cwl/tests/federation/testcase.cwl
+++ b/sdk/cwl/tests/federation/framework/testcase.cwl
@@ -25,14 +25,22 @@ inputs:
acr: string?
wf: File
obj: Any
- scrub_images: string[]
+ scrub_image: string
scrub_collections: string[]
runner_cluster: string?
outputs:
out:
type: Any
outputSource: run-acr/out
+ success:
+ type: boolean
+ outputSource: check-result/success
steps:
+ dockerbuild:
+ in:
+ testcase: scrub_image
+ out: [imagename]
+ run: dockerbuild.cwl
prepare:
in:
arvados_api_token: arvados_api_token
@@ -41,13 +49,14 @@ steps:
arvados_cluster_ids: arvados_cluster_ids
wf: wf
obj: obj
- scrub_images: scrub_images
+ scrub_image: scrub_image
scrub_collections: scrub_collections
out: [done]
run: prepare.cwl
run-acr:
in:
prepare: prepare/done
+ image-ready: dockerbuild/imagename
arvados_api_token: arvados_api_token
arvado_api_host_insecure: arvado_api_host_insecure
arvados_api_host: {source: arvados_api_hosts, valueFrom: "$(self[0])"}
@@ -57,3 +66,12 @@ steps:
obj: obj
out: [out]
run: run-acr.cwl
+ check-result:
+ in:
+ acr-done: run-acr/out
+ arvados_api_token: arvados_api_token
+ arvado_api_host_insecure: arvado_api_host_insecure
+ arvados_api_host: {source: arvados_api_hosts, valueFrom: "$(self[0])"}
+ check_collections: scrub_collections
+ out: [success]
+ run: check-exist.cwl
\ No newline at end of file
diff --git a/sdk/cwl/tests/federation/main.cwl b/sdk/cwl/tests/federation/main.cwl
index 4029d53d5..1042350f9 100755
--- a/sdk/cwl/tests/federation/main.cwl
+++ b/sdk/cwl/tests/federation/main.cwl
@@ -23,14 +23,22 @@ inputs:
arvados_api_hosts: string[]
arvados_cluster_ids: string[]
acr: string?
-
+ testcases:
+ type: string[]
+ default:
+ - base-case
+ - runner-home-step-remote
+ - runner-remote-step-home
outputs:
- base-case-out:
+ base-case-success:
+ type: Any
+ outputSource: base-case/success
+ runner-home-step-remote-success:
type: Any
- outputSource: base-case/out
- runner-home-step-remote-out:
+ outputSource: runner-home-step-remote/success
+ runner-remote-step-home-success:
type: Any
- outputSource: runner-home-step-remote/out
+ outputSource: runner-remote-step-home/success
steps:
base-case:
@@ -40,21 +48,31 @@ steps:
arvados_api_hosts: arvados_api_hosts
arvados_cluster_ids: arvados_cluster_ids
acr: acr
- wf: {default: {class: File, location: md5sum.cwl}}
+ wf:
+ default:
+ class: File
+ location: cases/base-case.cwl
+ secondaryFiles:
+ - class: File
+ location: cases/md5sum.cwl
obj:
default:
inp:
class: File
- location: whale.txt
+ location: data/base-case-input.txt
valueFrom: |-
${
self["runOnCluster"] = inputs.arvados_cluster_ids[0];
return self;
}
- scrub_images: {default: ["debian:9"]}
- scrub_collections: {default: ["cba47aefe5eb3a014a26ec00316b30c1+57", "67beab1cda8fe7d7e623323dc4287b5b+51"]}
- out: [out]
- run: testcase.cwl
+ scrub_image: {default: "arvados/fed-test:base-case"}
+ scrub_collections:
+ default:
+ - 031a4ced0aa99de90fb630568afc6e9b+67 # input collection
+ - eb93a6718eb1a1a8ee9f66ee7d683472+51 # md5sum output collection
+ - f654d4048612135f4a5e7707ec0fcf3e+112 # final output json
+ out: [out, success]
+ run: framework/testcase.cwl
runner-home-step-remote:
in:
@@ -63,22 +81,32 @@ steps:
arvados_api_hosts: arvados_api_hosts
arvados_cluster_ids: arvados_cluster_ids
acr: acr
- wf: {default: {class: File, location: md5sum.cwl}}
+ wf:
+ default:
+ class: File
+ location: cases/runner-home-step-remote.cwl
+ secondaryFiles:
+ - class: File
+ location: cases/md5sum.cwl
obj:
default:
inp:
class: File
- location: whale.txt
+ location: data/runner-home-step-remote-input.txt
valueFrom: |-
${
self["runOnCluster"] = inputs.arvados_cluster_ids[1];
return self;
}
runner_cluster: { valueFrom: "$(inputs.arvados_cluster_ids[0])" }
- scrub_images: {default: ["debian:9"]}
- scrub_collections: {default: ["cba47aefe5eb3a014a26ec00316b30c1+57", "67beab1cda8fe7d7e623323dc4287b5b+51"]}
- out: [out]
- run: testcase.cwl
+ scrub_image: {default: "arvados/fed-test:runner-home-step-remote"}
+ scrub_collections:
+ default:
+ - 3bc373e38751fe13dcbd62778d583242+81 # input collection
+ - 428e6d91e41a3af3ae287b453949e7fd+51 # md5sum output collection
+ - a4b0ddd866525655e8480f83a1ca83c6+112 # runner output json
+ out: [out, success]
+ run: framework/testcase.cwl
runner-remote-step-home:
in:
@@ -87,19 +115,29 @@ steps:
arvados_api_hosts: arvados_api_hosts
arvados_cluster_ids: arvados_cluster_ids
acr: acr
- wf: {default: {class: File, location: md5sum.cwl}}
+ wf:
+ default:
+ class: File
+ location: cases/runner-remote-step-home.cwl
+ secondaryFiles:
+ - class: File
+ location: cases/md5sum.cwl
obj:
default:
inp:
class: File
- location: whale.txt
+ location: data/runner-remote-step-home-input.txt
valueFrom: |-
${
self["runOnCluster"] = inputs.arvados_cluster_ids[0];
return self;
}
runner_cluster: { valueFrom: "$(inputs.arvados_cluster_ids[1])" }
- scrub_images: {default: ["debian:9"]}
- scrub_collections: {default: ["cba47aefe5eb3a014a26ec00316b30c1+57", "67beab1cda8fe7d7e623323dc4287b5b+51"]}
- out: [out]
- run: testcase.cwl
+ scrub_image: {default: "arvados/fed-test:runner-remote-step-home"}
+ scrub_collections:
+ default:
+ - 25fe10d8e8530329a738de69d9bc8ab5+81 # input collection
+ - 7f052d1a04b851b6f73fba77c7802e1d+51 # md5sum output collection
+ - ecb639201f454b6493757f5117f540df+112 # runner output json
+ out: [out, success]
+ run: framework/testcase.cwl
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