Add test for SchemaDefRequirement with a workflow and the types containing an $import statement #171
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It would be a better test if it did output something related to the custom types, yes. |
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Roger that, will keep that in mind for future PR's :-) thanks |
kinow
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conformance_tests.yaml
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| - tool: tests/schemadef_types_with_import-wf.cwl | ||
| job: tests/schemadef_types_with_import-job.json | ||
| output: { | ||
| "out": "ordereddict([('CN', 'UNKNOWN'), ('DT', '1970-01-01T00:00:00Z'), ('ID', 'SRR622461'), ('LB', 'Illumina NA12878'), ('PI', '250'), ('PL', 'ILLUMINA'), ('SM', 'NA12878')])\n" |
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out here was interesting. In tests/schemadef_types_with_import-tool.cwl I used valueFrom: $(self.readgroup_meta_list) and it returned the repr of the ordered dict (I think).
If I used valueFrom: $(self.readgroup_meta_list)[] then the ordereddict prefix was gone 😕
What I wanted was to access DT or ID for the echo command. Any idea if that's doable?
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That's a cwltool bug, the serialization should be a pure JSON object. Can you open an issue with a reproducer?
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Creating the smallest example to reproduce the issue, then will create the issue (and maybe a PR too).
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| - id: message | ||
| type: "schemadef_types_with_import_readgroup.yml#readgroups_bam_file" | ||
| inputBinding: | ||
| valueFrom: $(self.readgroup_meta_list) |
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If you want the value of DT, you could try this:
| valueFrom: $(self.readgroup_meta_list) | |
| valueFrom: $(self.readgroup_meta_list["DT"]) |
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That almost worked. But the error message displayed the read_group_meta_list that made me realize we had type: array in the input type. So $(self.readgroup_meta_list[0]['DT']) did the trick 👍 thanks @mr-c !
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…ining an $import statement. Used example written by @jeremiahsavage (thanks!)
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Created |
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Thanks! |
For common-workflow-language/common-workflow-language#703
Used example written by @jeremiahsavage (thanks!). It doesn't output anything, but validates that it could import the types successfully.
Or if we prefer to test for some output, I can rewrite it to output something.
Cheers
Bruno