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CWL workflow steps #649
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Merged
CWL workflow steps #649
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… Multiple Input requirements
…ements strict validation
…bworkflowFeatureRequirement validation
… + support CWL loadContent with expression + align ESGF with WpsProcessBase methods
…tputs + update changelog
…onsitent progress
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #649 +/- ##
==========================================
- Coverage 85.78% 85.76% -0.02%
==========================================
Files 79 79
Lines 18654 18846 +192
Branches 2862 2905 +43
==========================================
+ Hits 16002 16163 +161
- Misses 1907 1927 +20
- Partials 745 756 +11 ☔ View full report in Codecov by Sentry. |
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Labels
ci/doc
Issue related to documentation of the package
ci/operations
Related to CI operations (actions, execution, install, builds, etc.)
ci/tests
Tests of the package and features
feature/CWL
Issue related to CWL support
feature/oas
Issues related to OpenAPI specifications.
process/esgf-cwt
Issue related to ESGF-CWT components.
process/workflow
Related to a Workflow process.
process/wps1
Issue related to WPS 1.x processes support
process/wps3
Issue related to WPS 3.x (REST-JSON) processes support
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Changes:
CWL
MultipleInputFeatureRequirement
support.CWL
SubworkflowFeatureRequirement
support.CWL
Workflow
explicit schema validation of itssteps
.CWL
requirements
. Only fully defined and resolved definitions will be allowed.If an unsupported
CWL
requirement byWeaver
must be provided (but is a valid definition supported bycwltool
),it must now be provided through
hints
to succeed schema validation.CWL
output definition usingloadContents
to anoutputBinding.glob
reference toload the
File
contents into astring
output.CWL
JavaScript expressions within intermediate steps of aWorkflow
to collect output resultsfrom relevant sources with better data manipulation flexibility.
weaver.processes.wps_process_base.WpsProcessInterface
to allow better reuse of thecommon operations shared by derived
CWL
Workflow
steps implemented byESGFProcess
,Wps1Process
,Wps3Process
andOGCAPIRemoteProcessBase
.ESGFProcess
to use the common operations ofCWL
Workflow
steps defined byWpsProcessInterface
.Fixes:
CWL
schema definition forScatterFeatureRequirement
that directlycontained the corresponding fields
scatter
andscatterMethod
, instead of the expecteddefinition within a
Workflow Step
.CWL
requirements
schema definition usingOneOf
and thediscriminator
property that could sometimedrop a definition when it only contained an empty mapping
{}
, and that the corresponding requirement allows it.weaver.wps_restapi.colander_extras.AnyOfKeywordSchema
not allowing distinctJSON
structuretype
to becombined simultaneously.
CWL
Workflow
not retrieving output results when returned directly as literal data from a remoteProcess
.CWL
Workflow
potentially failing tool resolution for a local stepProcess
ifhints
where omitted.CWL
Workflow
resolution of steprequirements
from one of theWeaver
application types(i.e.:
builtin
,docker
,ESGF-CWT
,OGCAPI
,WPS1
) due tocwltool
namespace adding aprefixed URI.