[ARVADOS] updated: 2.1.0-1283-g93be5ba7e
Git user
git at public.arvados.org
Tue Sep 7 18:59:25 UTC 2021
Summary of changes:
doc/user/cwl/cwl-extensions.html.textile.liquid | 13 ++++++++++
sdk/cwl/arvados_cwl/__init__.py | 3 ++-
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.0.yml | 34 +++++++++++++++++++++++++
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.1.yml | 34 +++++++++++++++++++++++++
sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml | 6 ++---
sdk/cwl/tests/test_submit.py | 4 +--
6 files changed, 88 insertions(+), 6 deletions(-)
via 93be5ba7e96f1a62f53aee8c1e4979a99d1a9d94 (commit)
via 670ba06e9ca3b1a84c88b6d69a36a575df95cb44 (commit)
from 97e0090ec440c3322053d7635d883cf8af6633ca (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 93be5ba7e96f1a62f53aee8c1e4979a99d1a9d94
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Tue Sep 7 14:59:11 2021 -0400
14018: Add ProcessProperties to documentation
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/doc/user/cwl/cwl-extensions.html.textile.liquid b/doc/user/cwl/cwl-extensions.html.textile.liquid
index 206b75d58..6a70454b1 100644
--- a/doc/user/cwl/cwl-extensions.html.textile.liquid
+++ b/doc/user/cwl/cwl-extensions.html.textile.liquid
@@ -52,6 +52,11 @@ hints:
arv:OutputStorageClass:
intermediateStorageClass: fast_storage
finalStorageClass: robust_storage
+
+ arv:ProcessProperties:
+ processProperties:
+ property1: value1
+ property2: $(inputs.value2)
{% endcodeblock %}
h2(#RunInSingleContainer). arv:RunInSingleContainer
@@ -134,6 +139,14 @@ table(table table-bordered table-condensed).
|intermediateStorageClass|string or array of strings|The storage class for output of intermediate steps. For example, faster "hot" storage.|
|finalStorageClass_uuid|string or array of strings|The storage class for the final output. |
+h2(#ProcessProperties). arv:ProcessProperties
+
+Specify extra "properties":{{site.baseurl}}/api/methods.html#subpropertyfilters that will be set on container requests created by the workflow. May be set on a Workflow or a CommandLineTool. Setting custom properties on a container request simplifies queries to find the workflow run later on.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|processProperties|key-value map, or list of objects with the fields {propertyName, propertyValue}|The properties that will be set on the container request. May include expressions that reference `$(inputs)` of the current workflow or tool.|
+
h2. arv:dockerCollectionPDH
This is an optional extension field appearing on the standard @DockerRequirement at . It specifies the portable data hash of the Arvados collection containing the Docker image. If present, it takes precedence over @dockerPull@ or @dockerImageId at .
commit 670ba06e9ca3b1a84c88b6d69a36a575df95cb44
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Tue Sep 7 14:45:40 2021 -0400
14018: Add arv:ProcessProperties to all the extension schemas.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 7bbb3b29e..ee636be37 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -249,7 +249,8 @@ def add_arv_hints():
"http://arvados.org/cwl#IntermediateOutput",
"http://arvados.org/cwl#ReuseRequirement",
"http://arvados.org/cwl#ClusterTarget",
- "http://arvados.org/cwl#OutputStorageClass"
+ "http://arvados.org/cwl#OutputStorageClass",
+ "http://arvados.org/cwl#ProcessProperties"
])
def exit_signal_handler(sigcode, frame):
diff --git a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.0.yml b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.0.yml
index 2a2e857e0..bc5aeaf79 100644
--- a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.0.yml
+++ b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.0.yml
@@ -295,3 +295,37 @@ $graph:
- type: array
items: string
doc: One or more storages classes
+
+- type: record
+ name: PropertyDef
+ doc: |
+ Define a property that will be set on the submitted container
+ request associated with this workflow or step.
+ fields:
+ - name: propertyName
+ type: string
+ doc: The property key
+ - name: propertyValue
+ type: [Any]
+ doc: The property value
+
+
+- name: ProcessProperties
+ type: record
+ extends: cwl:ProcessRequirement
+ inVocab: false
+ doc: |
+ Specify metadata properties that will be set on the submitted
+ container request associated with this workflow or step.
+ fields:
+ class:
+ type: string
+ doc: "Always 'arv:ProcessProperties"
+ jsonldPredicate:
+ _id: "@type"
+ _type: "@vocab"
+ processProperties:
+ type: PropertyDef[]
+ jsonldPredicate:
+ mapSubject: propertyName
+ mapPredicate: propertyValue
diff --git a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.1.yml b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.1.yml
index fb14a63e3..a60ead113 100644
--- a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.1.yml
+++ b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.1.yml
@@ -238,3 +238,37 @@ $graph:
- type: array
items: string
doc: One or more storages classes
+
+- type: record
+ name: PropertyDef
+ doc: |
+ Define a property that will be set on the submitted container
+ request associated with this workflow or step.
+ fields:
+ - name: propertyName
+ type: string
+ doc: The property key
+ - name: propertyValue
+ type: [Any]
+ doc: The property value
+
+
+- name: ProcessProperties
+ type: record
+ extends: cwl:ProcessRequirement
+ inVocab: false
+ doc: |
+ Specify metadata properties that will be set on the submitted
+ container request associated with this workflow or step.
+ fields:
+ class:
+ type: string
+ doc: "Always 'arv:ProcessProperties"
+ jsonldPredicate:
+ _id: "@type"
+ _type: "@vocab"
+ processProperties:
+ type: PropertyDef[]
+ jsonldPredicate:
+ mapSubject: propertyName
+ mapPredicate: propertyValue
diff --git a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml
index 09951a984..a34ef3342 100644
--- a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml
+++ b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml
@@ -271,6 +271,6 @@ $graph:
_type: "@vocab"
processProperties:
type: PropertyDef[]
- #jsonldPredicate:
- # mapSubject: propertyName
- # mapPredicate: propertyValue
+ jsonldPredicate:
+ mapSubject: propertyName
+ mapPredicate: propertyValue
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 2889ce331..8c0fcaf74 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -1432,10 +1432,10 @@ class TestSubmit(unittest.TestCase):
{
"class": "http://arvados.org/cwl#ProcessProperties",
"processProperties": [
- {"propertyName": "foo",
- "propertyValue": "bar"},
{"propertyName": "baz",
"propertyValue": "$(inputs.x.basename)"},
+ {"propertyName": "foo",
+ "propertyValue": "bar"},
{"propertyName": "quux",
"propertyValue": {
"q1": 1,
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