Comments (8)
The first workflow exception message and stack trace is >600 lines long, below is an abbreviated version:
! org.w3id.cwl.cwl1_2.utils.ValidationException: Failed to match union type
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@270f831a
! the `inputs` field is not valid because:
! Failed to match union type
! Expected object with Java type of java.util.List but got java.util.HashMap
! Trying 'RecordField'
! the `type` field is not valid because:
! Failed to match union type
! Expected object with Java type of java.lang.String but got java.util.LinkedHashMap
! Expected object with Java type of java.lang.String but got java.util.LinkedHashMap
! Trying 'RecordField'
! the `type` field is not valid because:
! Expected one of [Ljava.lang.String;@65553746
! Trying 'RecordField'
! the `symbols` field is not valid because:
! Expected object with Java type of java.util.List but got null
! the `type` field is not valid because:
! Expected one of [Ljava.lang.String;@61bee517
! Trying 'RecordField'
[ many lines deleted ]
! Trying 'RecordField'
! the `symbols` field is not valid because:
! Expected object with Java type of java.util.List but got null
! the `type` field is not valid because:
! Expected one of [Ljava.lang.String;@61bee517
! Trying 'RecordField'
! the `items` field is not valid because:
! TumourType.yaml#TumourType
! Expected object with Java type of java.lang.String but got java.util.LinkedHashMap
! Expected object with Java type of java.util.List but got java.util.LinkedHashMap
! Expected object with Java type of java.util.List but got java.util.LinkedHashMap
! at org.w3id.cwl.cwl1_2.utils.UnionLoader.load(UnionLoader.java:31)
! at org.w3id.cwl.cwl1_2.utils.Loader.documentLoad(Loader.java:41)
! at org.w3id.cwl.cwl1_2.utils.RootLoader.loadDocument(RootLoader.java:18)
from cwljava.
The second workflow exception message and stack trace:
! org.w3id.cwl.cwl1_2.utils.ValidationException: Failed to match union type
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@176252b7
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@6668dafa
! the `expression` field is not valid because:
! Expected a string.
! Trying 'RecordField'
! the `steps` field is not valid because:
! Failed to match union type
! Expected object with Java type of java.util.List but got java.util.HashMap
! Trying 'RecordField'
! the `run` field is not valid because:
! Failed to match union type
! Expected object with Java type of java.lang.String but got java.util.LinkedHashMap
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@176252b7
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@6668dafa
! the `expression` field is not valid because:
! Expected a string.
! Trying 'RecordField'
! the `steps` field is not valid because:
! Failed to match union type
! Expected object with Java type of java.util.List but got java.util.HashMap
! Trying 'RecordField'
! the `run` field is not valid because:
! Failed to match union type
! Expected object with Java type of java.lang.String but got java.util.LinkedHashMap
! Trying 'RecordField'
! the `cwlVersion` field is not valid because:
! Expected one of [Ljava.lang.String;@5871ac54
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@6668dafa
! the `cwlVersion` field is not valid because:
! Expected one of [Ljava.lang.String;@5871ac54
! the `expression` field is not valid because:
! Expected a string.
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@13467c17
! the `cwlVersion` field is not valid because:
! Expected one of [Ljava.lang.String;@5871ac54
! the `steps` field is not valid because:
! Expected object with Java type of java.util.List but got null
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@1f20d341
! the `cwlVersion` field is not valid because:
! Expected one of [Ljava.lang.String;@5871ac54
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@1f20d341
! Trying 'RecordField'
! the `class` field is not valid because:
! Expected one of [Ljava.lang.String;@1f20d341
! Expected object with Java type of java.util.List but got java.util.LinkedHashMap
! at org.w3id.cwl.cwl1_2.utils.UnionLoader.load(UnionLoader.java:31)
! at org.w3id.cwl.cwl1_2.utils.Loader.documentLoad(Loader.java:41)
! at org.w3id.cwl.cwl1_2.utils.RootLoader.loadDocument(RootLoader.java:18)
from cwljava.
Hello @svonworl ; cwljava
is currently only for CWL v1.2; if you'd like to parse CWL v1.1 and CWL v1.0 documents, that will have to be added as separate packages; you'll likely want code to dispatch to the correct loader based upon the cwlVersion
from cwljava.
@mr-c, are you planning to add support for 1.1 and 1.0? How much work would it be if we wanted to contribute that support ourselves (I haven't really looked at the codebase)?
from cwljava.
@coverbeck I did a quick stab at CWL v1.1 in #105 (including a bit of documentation)
Would you like to take over the branch and continue with adding CWL v1.0 as well?
from cwljava.
@mr-c , at this point we're still trying to figure out how/if we want to integrate cwljava with Dockstore. We couldn't commit to any work, at least not yet.
414 files in the PR! :) Presumably most of those are generated? Otherwise it seems like a massive undertaking. :)
from cwljava.
@mr-c , at this point we're still trying to figure out how/if we want to integrate cwljava with Dockstore. We couldn't commit to any work, at least not yet.
414 files in the PR! :) Presumably most of those are generated? Otherwise it seems like a massive undertaking. :)
It is almost entirely automated, yes 😅
See https://github.com/common-workflow-language/cwljava/pull/105/files
from cwljava.
Support for CWL v1.1 was added in #105 ; I can do the same for CWL v1.0, if someone requests it
from cwljava.
Related Issues (20)
- Partial/lazy parse? HOT 3
- Supporting recursive expansion of `typeDSL`
- Incomplete $import support HOT 5
- Fails to parse conformance tests (ValidationException: Failed to match union type) HOT 4
- SchemaDefRequirement not parsed correctly HOT 2
- Fails to parse requirements correctly HOT 5
- No way to access custom metadata HOT 2
- Workflows are not parsed correctly HOT 1
- NullPointerException HOT 1
- Add Apache 2.0 license
- CWL version is not set when parsing a packed workflow HOT 4
- Workflow with imported schema is not parsable when packed HOT 1
- Add helper to upgrade documents to CWL v1.2
- WorkflowStepInput source IDs incorrect when parsing workflow packed with cwlpack HOT 5
- Embedded process ID is ignored HOT 2
- Enum types are not parsed correctly HOT 6
- secondaryFiles with pattern cannot be parsed when given in workflow inputs HOT 4
- explore rendering the markdown in the javadocs
- Using this SDK to generate CWL Documents HOT 5
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from cwljava.