[ARVADOS] updated: 1.1.3-258-g8680023
Git user
git at public.curoverse.com
Mon Apr 2 14:31:23 EDT 2018
Summary of changes:
sdk/cwl/tests/arvados-tests.yml | 25 +++++++++++++++++++++++++
sdk/cwl/tests/wf/runin-reqs-wf.cwl | 26 ++++++++++++++++++--------
sdk/cwl/tests/wf/runin-reqs-wf2.cwl | 29 +++++++++++++++++++----------
sdk/cwl/tests/wf/runin-reqs-wf3.cwl | 27 ++++++++++++++++++---------
sdk/cwl/tests/wf/runin-reqs-wf4.cwl | 25 +++++++++++++++++--------
5 files changed, 97 insertions(+), 35 deletions(-)
via 8680023bb3804d3bd1f2dcac7d1a86ff14053fca (commit)
from 48a362bb93d1e53e879a563da85aecd070987f30 (commit)
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commit 8680023bb3804d3bd1f2dcac7d1a86ff14053fca
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Mon Apr 2 14:30:54 2018 -0400
Add RunInSingleContainer dynamic resource request tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index ea6477c..87db44b 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -146,3 +146,28 @@
}
tool: wf/secret_wf.cwl
doc: "Test secret input parameters"
+
+- job: null
+ output:
+ out: null
+ tool: wf/runin-reqs-wf.cwl
+ doc: "RunInSingleContainer handles dynamic resource requests on step"
+
+- job: null
+ output:
+ out: null
+ tool: wf/runin-reqs-wf2.cwl
+ doc: "RunInSingleContainer handles dynamic resource requests on embedded subworkflow"
+
+- job: null
+ output:
+ out: null
+ tool: wf/runin-reqs-wf3.cwl
+ should_fail: true
+ doc: "RunInSingleContainer disallows dynamic resource request on subworkflow steps"
+
+- job: null
+ output:
+ out: null
+ tool: wf/runin-reqs-wf4.cwl
+ doc: "RunInSingleContainer discovers static resource request in subworkflow steps"
diff --git a/sdk/cwl/tests/wf/runin-reqs-wf.cwl b/sdk/cwl/tests/wf/runin-reqs-wf.cwl
index 8e3557e..9032e26 100644
--- a/sdk/cwl/tests/wf/runin-reqs-wf.cwl
+++ b/sdk/cwl/tests/wf/runin-reqs-wf.cwl
@@ -7,9 +7,14 @@ cwlVersion: v1.0
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
- sleeptime:
+ count:
type: int[]
default: [1, 2, 3, 4]
+ script:
+ type: File
+ default:
+ class: File
+ location: check_mem.py
outputs:
out: []
requirements:
@@ -20,29 +25,34 @@ requirements:
steps:
substep:
in:
- sleeptime: sleeptime
+ count: count
+ script: script
out: []
hints:
- class: arv:RunInSingleContainer
- class: ResourceRequirement
- ramMin: $(inputs.sleeptime*4)
- scatter: sleeptime
+ ramMin: $(inputs.count*4)
+ - class: arv:APIRequirement
+ scatter: count
run:
class: Workflow
id: mysub
inputs:
- sleeptime: int
+ count: int
+ script: File
outputs: []
steps:
sleep1:
in:
- sleeptime: sleeptime
+ count: count
+ script: script
out: []
run:
class: CommandLineTool
id: subtool
inputs:
- sleeptime:
+ count:
type: int
+ script: File
outputs: []
- baseCommand: [cat, /proc/meminfo]
+ arguments: [python, $(inputs.script), $(inputs.count * 4)]
diff --git a/sdk/cwl/tests/wf/runin-reqs-wf2.cwl b/sdk/cwl/tests/wf/runin-reqs-wf2.cwl
index 50db901..cc1321a 100644
--- a/sdk/cwl/tests/wf/runin-reqs-wf2.cwl
+++ b/sdk/cwl/tests/wf/runin-reqs-wf2.cwl
@@ -7,9 +7,14 @@ cwlVersion: v1.0
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
- sleeptime:
+ count:
type: int[]
default: [1, 2, 3, 4]
+ script:
+ type: File
+ default:
+ class: File
+ location: check_mem.py
outputs:
out: []
requirements:
@@ -20,31 +25,35 @@ requirements:
steps:
substep:
in:
- sleeptime: sleeptime
+ count: count
+ script: script
out: []
hints:
- class: arv:RunInSingleContainer
- scatter: sleeptime
+ - class: arv:APIRequirement
+ scatter: count
run:
class: Workflow
id: mysub
inputs:
- sleeptime: int
+ count: int
+ script: File
outputs: []
hints:
- - class: ResourceRequirement
- ramMin: $(inputs.sleeptime*4)
+ - class: ResourceRequirement
+ ramMin: $(inputs.count*4)
steps:
sleep1:
in:
- sleeptime: sleeptime
+ count: count
+ script: script
out: []
run:
class: CommandLineTool
id: subtool
inputs:
- sleeptime:
+ count:
type: int
- inputBinding: {position: 1}
+ script: File
outputs: []
- baseCommand: sleep
+ arguments: [python, $(inputs.script), $(inputs.count * 4)]
diff --git a/sdk/cwl/tests/wf/runin-reqs-wf3.cwl b/sdk/cwl/tests/wf/runin-reqs-wf3.cwl
index 352a919..92bf482 100644
--- a/sdk/cwl/tests/wf/runin-reqs-wf3.cwl
+++ b/sdk/cwl/tests/wf/runin-reqs-wf3.cwl
@@ -7,9 +7,14 @@ cwlVersion: v1.0
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
- sleeptime:
+ count:
type: int[]
default: [1, 2, 3, 4]
+ script:
+ type: File
+ default:
+ class: File
+ location: check_mem.py
outputs:
out: []
requirements:
@@ -20,31 +25,35 @@ requirements:
steps:
substep:
in:
- sleeptime: sleeptime
+ count: count
+ script: script
out: []
hints:
- class: arv:RunInSingleContainer
- scatter: sleeptime
+ - class: arv:APIRequirement
+ scatter: count
run:
class: Workflow
id: mysub
inputs:
- sleeptime: int
+ count: int
+ script: File
outputs: []
steps:
sleep1:
in:
- sleeptime: sleeptime
+ count: count
+ script: script
out: []
run:
class: CommandLineTool
id: subtool
hints:
- class: ResourceRequirement
- ramMin: $(inputs.sleeptime*4)
+ ramMin: $(inputs.count*4)
inputs:
- sleeptime:
+ count:
type: int
- inputBinding: {position: 1}
+ script: File
outputs: []
- baseCommand: sleep
+ arguments: [python, $(inputs.script), $(inputs.count * 4)]
diff --git a/sdk/cwl/tests/wf/runin-reqs-wf4.cwl b/sdk/cwl/tests/wf/runin-reqs-wf4.cwl
index 75f50d2..b7a9779 100644
--- a/sdk/cwl/tests/wf/runin-reqs-wf4.cwl
+++ b/sdk/cwl/tests/wf/runin-reqs-wf4.cwl
@@ -7,9 +7,14 @@ cwlVersion: v1.0
$namespaces:
arv: "http://arvados.org/cwl#"
inputs:
- sleeptime:
+ count:
type: int[]
default: [1, 2, 3, 4]
+ script:
+ type: File
+ default:
+ class: File
+ location: check_mem.py
outputs:
out: []
requirements:
@@ -20,21 +25,25 @@ requirements:
steps:
substep:
in:
- sleeptime: sleeptime
+ count: count
+ script: script
out: []
hints:
- class: arv:RunInSingleContainer
- scatter: sleeptime
+ - class: arv:APIRequirement
+ scatter: count
run:
class: Workflow
id: mysub
inputs:
- sleeptime: int
+ count: int
+ script: File
outputs: []
steps:
sleep1:
in:
- sleeptime: sleeptime
+ count: count
+ script: script
out: []
run:
class: CommandLineTool
@@ -43,8 +52,8 @@ steps:
- class: ResourceRequirement
ramMin: 8
inputs:
- sleeptime:
+ count:
type: int
- inputBinding: {position: 1}
+ script: File
outputs: []
- baseCommand: sleep
+ arguments: [python, $(inputs.script), "8"]
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