[ARVADOS] updated: 1.2.0-330-g295907e54
Git user
git at public.curoverse.com
Fri Nov 9 10:47:36 EST 2018
Summary of changes:
sdk/cwl/tests/federation/cases/base-case.cwl | 3 +-
sdk/cwl/tests/federation/cases/md5sum.cwl | 3 ++
.../tests/federation/cases/{md5sum.cwl => rev.cwl} | 8 ++--
.../federation/cases/runner-home-step-remote.cwl | 3 +-
.../federation/cases/runner-remote-step-home.cwl | 3 +-
...te-step-home.cwl => twostep-home-to-remote.cwl} | 19 +++++++---
...te-step-home.cwl => twostep-remote-to-home.cwl} | 14 +++++--
...e-case-input.txt => twostep-home-to-remote.txt} | 2 +-
...e-case-input.txt => twostep-remote-to-home.txt} | 2 +-
sdk/cwl/tests/federation/framework/prepare.py | 2 +-
sdk/cwl/tests/federation/main.cwl | 43 ++++++++++++++++++++++
11 files changed, 81 insertions(+), 21 deletions(-)
copy sdk/cwl/tests/federation/cases/{md5sum.cwl => rev.cwl} (73%)
copy sdk/cwl/tests/federation/cases/{runner-remote-step-home.cwl => twostep-home-to-remote.cwl} (54%)
copy sdk/cwl/tests/federation/cases/{runner-remote-step-home.cwl => twostep-remote-to-home.cwl} (65%)
copy sdk/cwl/tests/federation/data/{base-case-input.txt => twostep-home-to-remote.txt} (92%)
copy sdk/cwl/tests/federation/data/{base-case-input.txt => twostep-remote-to-home.txt} (92%)
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from 448138a8a6311076dbca802aaa5ea1e624c63d29 (commit)
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commit 295907e5496eb5a3661ecfffd026c3f7aa6a053f
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Fri Nov 9 10:47:23 2018 -0500
14198: Working on two step test cases
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/federation/cases/base-case.cwl b/sdk/cwl/tests/federation/cases/base-case.cwl
index 2e0ff64c6..57eff5975 100644
--- a/sdk/cwl/tests/federation/cases/base-case.cwl
+++ b/sdk/cwl/tests/federation/cases/base-case.cwl
@@ -10,8 +10,6 @@ requirements:
InlineJavascriptRequirement: {}
DockerRequirement:
dockerPull: arvados/fed-test:base-case
- arv:ClusterTarget:
- cluster_id: $(inputs.runOnCluster)
inputs:
inp:
type: File
@@ -25,5 +23,6 @@ steps:
md5sum:
in:
inp: inp
+ runOnCluster: runOnCluster
out: [hash]
run: md5sum.cwl
\ No newline at end of file
diff --git a/sdk/cwl/tests/federation/cases/md5sum.cwl b/sdk/cwl/tests/federation/cases/md5sum.cwl
index af119990a..8a844e9dd 100644
--- a/sdk/cwl/tests/federation/cases/md5sum.cwl
+++ b/sdk/cwl/tests/federation/cases/md5sum.cwl
@@ -8,9 +8,12 @@ $namespaces:
arv: "http://arvados.org/cwl#"
requirements:
InlineJavascriptRequirement: {}
+ arv:ClusterTarget:
+ cluster_id: $(inputs.runOnCluster)
inputs:
inp:
type: File
+ runOnCluster: string
outputs:
hash:
type: File
diff --git a/sdk/cwl/tests/federation/cases/md5sum.cwl b/sdk/cwl/tests/federation/cases/rev.cwl
similarity index 73%
copy from sdk/cwl/tests/federation/cases/md5sum.cwl
copy to sdk/cwl/tests/federation/cases/rev.cwl
index af119990a..13e7a87f2 100644
--- a/sdk/cwl/tests/federation/cases/md5sum.cwl
+++ b/sdk/cwl/tests/federation/cases/rev.cwl
@@ -8,14 +8,16 @@ $namespaces:
arv: "http://arvados.org/cwl#"
requirements:
InlineJavascriptRequirement: {}
+ arv:ClusterTarget:
+ cluster_id: $(inputs.runOnCluster)
inputs:
inp:
type: File
+ runOnCluster: string
outputs:
- hash:
+ revhash:
type: File
outputBinding:
glob: out.txt
-stdin: $(inputs.inp.path)
stdout: out.txt
-arguments: ["md5sum", "-"]
+arguments: [rev, $(inputs.inp)]
diff --git a/sdk/cwl/tests/federation/cases/runner-home-step-remote.cwl b/sdk/cwl/tests/federation/cases/runner-home-step-remote.cwl
index 70d017639..0621dd736 100644
--- a/sdk/cwl/tests/federation/cases/runner-home-step-remote.cwl
+++ b/sdk/cwl/tests/federation/cases/runner-home-step-remote.cwl
@@ -10,8 +10,6 @@ requirements:
InlineJavascriptRequirement: {}
DockerRequirement:
dockerPull: arvados/fed-test:runner-home-step-remote
- arv:ClusterTarget:
- cluster_id: $(inputs.runOnCluster)
inputs:
inp:
type: File
@@ -25,5 +23,6 @@ steps:
md5sum:
in:
inp: inp
+ runOnCluster: runOnCluster
out: [hash]
run: md5sum.cwl
\ No newline at end of file
diff --git a/sdk/cwl/tests/federation/cases/runner-remote-step-home.cwl b/sdk/cwl/tests/federation/cases/runner-remote-step-home.cwl
index 33681f18e..6ce3cce41 100644
--- a/sdk/cwl/tests/federation/cases/runner-remote-step-home.cwl
+++ b/sdk/cwl/tests/federation/cases/runner-remote-step-home.cwl
@@ -10,8 +10,6 @@ requirements:
InlineJavascriptRequirement: {}
DockerRequirement:
dockerPull: arvados/fed-test:runner-remote-step-home
- arv:ClusterTarget:
- cluster_id: $(inputs.runOnCluster)
inputs:
inp:
type: File
@@ -25,5 +23,6 @@ steps:
md5sum:
in:
inp: inp
+ runOnCluster: runOnCluster
out: [hash]
run: md5sum.cwl
\ No newline at end of file
diff --git a/sdk/cwl/tests/federation/cases/base-case.cwl b/sdk/cwl/tests/federation/cases/twostep-home-to-remote.cwl
similarity index 54%
copy from sdk/cwl/tests/federation/cases/base-case.cwl
copy to sdk/cwl/tests/federation/cases/twostep-home-to-remote.cwl
index 2e0ff64c6..ffce6c3c4 100644
--- a/sdk/cwl/tests/federation/cases/base-case.cwl
+++ b/sdk/cwl/tests/federation/cases/twostep-home-to-remote.cwl
@@ -9,14 +9,13 @@ $namespaces:
requirements:
InlineJavascriptRequirement: {}
DockerRequirement:
- dockerPull: arvados/fed-test:base-case
- arv:ClusterTarget:
- cluster_id: $(inputs.runOnCluster)
+ dockerPull: arvados/fed-test:twostep-home-to-remote
inputs:
inp:
type: File
inputBinding: {}
- runOnCluster: string
+ md5sumCluster: string
+ revCluster: string
outputs:
hash:
type: File
@@ -25,5 +24,15 @@ steps:
md5sum:
in:
inp: inp
+ runOnCluster: md5sumCluster
out: [hash]
- run: md5sum.cwl
\ No newline at end of file
+ run: md5sum.cwl
+ rev:
+ in:
+ inp: md5sum/hash
+ runOnCluster: revCluster
+ out: [revhash]
+ run: rev.cwl
+ requirements:
+ arv:ClusterTarget:
+ cluster_id: $(inputs.runOnCluster)
diff --git a/sdk/cwl/tests/federation/cases/base-case.cwl b/sdk/cwl/tests/federation/cases/twostep-remote-to-home.cwl
similarity index 65%
copy from sdk/cwl/tests/federation/cases/base-case.cwl
copy to sdk/cwl/tests/federation/cases/twostep-remote-to-home.cwl
index 2e0ff64c6..4541ebba2 100644
--- a/sdk/cwl/tests/federation/cases/base-case.cwl
+++ b/sdk/cwl/tests/federation/cases/twostep-remote-to-home.cwl
@@ -9,9 +9,7 @@ $namespaces:
requirements:
InlineJavascriptRequirement: {}
DockerRequirement:
- dockerPull: arvados/fed-test:base-case
- arv:ClusterTarget:
- cluster_id: $(inputs.runOnCluster)
+ dockerPull: arvados/fed-test:twostep-remote-to-home
inputs:
inp:
type: File
@@ -26,4 +24,12 @@ steps:
in:
inp: inp
out: [hash]
- run: md5sum.cwl
\ No newline at end of file
+ run: md5sum.cwl
+ requirements:
+ arv:ClusterTarget:
+ cluster_id: $(inputs.runOnCluster)
+ rev:
+ in:
+ inp: md5sum/hash
+ out: [revhash]
+ run: rev.cwl
diff --git a/sdk/cwl/tests/federation/data/twostep-home-to-remote.txt b/sdk/cwl/tests/federation/data/twostep-home-to-remote.txt
new file mode 100644
index 000000000..6430ad509
--- /dev/null
+++ b/sdk/cwl/tests/federation/data/twostep-home-to-remote.txt
@@ -0,0 +1,16 @@
+Call me twostep-home-to-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
+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/twostep-remote-to-home.txt b/sdk/cwl/tests/federation/data/twostep-remote-to-home.txt
new file mode 100644
index 000000000..231802581
--- /dev/null
+++ b/sdk/cwl/tests/federation/data/twostep-remote-to-home.txt
@@ -0,0 +1,16 @@
+Call me twostep-remote-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/framework/prepare.py b/sdk/cwl/tests/federation/framework/prepare.py
index 94a6a75ed..52c780a87 100644
--- a/sdk/cwl/tests/federation/framework/prepare.py
+++ b/sdk/cwl/tests/federation/framework/prepare.py
@@ -33,10 +33,10 @@ for cluster_id in config["arvados_cluster_ids"]:
for lk in search_links["items"]:
api.links().delete(uuid=lk["uuid"]).execute()
-
for cluster_id in config["arvados_cluster_ids"]:
matches = api.collections().list(filters=[["portable_data_hash", "in", list(scrub_collections)]],
select=["uuid", "portable_data_hash"], cluster_id=cluster_id).execute()
+ print("matches from %s was %s" % (cluster_id, matches))
for m in matches["items"]:
api.collections().delete(uuid=m["uuid"]).execute()
print("Scrubbed %s (%s)" % (m["uuid"], m["portable_data_hash"]))
diff --git a/sdk/cwl/tests/federation/main.cwl b/sdk/cwl/tests/federation/main.cwl
index 1042350f9..346f97914 100755
--- a/sdk/cwl/tests/federation/main.cwl
+++ b/sdk/cwl/tests/federation/main.cwl
@@ -39,6 +39,9 @@ outputs:
runner-remote-step-home-success:
type: Any
outputSource: runner-remote-step-home/success
+ twostep-home-to-remote-success:
+ type: Any
+ outputSource: twostep-home-to-remote/success
steps:
base-case:
@@ -141,3 +144,43 @@ steps:
- ecb639201f454b6493757f5117f540df+112 # runner output json
out: [out, success]
run: framework/testcase.cwl
+
+ twostep-home-to-remote:
+ 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-home-to-remote.cwl
+ secondaryFiles:
+ - class: File
+ location: cases/md5sum.cwl
+ - class: File
+ location: cases/rev.cwl
+ obj:
+ default:
+ inp:
+ class: File
+ location: data/twostep-home-to-remote.txt
+ valueFrom: |-
+ ${
+ self["md5sumCluster"] = inputs.arvados_cluster_ids[0];
+ self["revCluster"] = inputs.arvados_cluster_ids[1];
+ return self;
+ }
+ runner_cluster: { valueFrom: "$(inputs.arvados_cluster_ids[0])" }
+ scrub_image: {default: "arvados/fed-test:twostep-home-to-remote"}
+ scrub_collections:
+ default:
+ - 268a54947fb75115cfe05bb54cc62c30+74 # input collection
+ - 400f03b8c5d2dc3dcb513a21b626ef88+51 # md5sum output collection
+ - 3738166916ca5f6f6ad12bf7e06b4a21+51 # rev output collection
+ - bc37c17a37aa25229e5de1339b27fbcc+112 # runner output json
+ out: [out, success]
+ run: framework/testcase.cwl
+
+ # also: twostep-all-remote
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