Allow relative imports from URL-submitted CWL #4308
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| def parse(): Parse[Cwl] = source.workflowUrl match { | ||
| case Some(url) => for { | ||
| reference <- fromEither[IO](CwlReference.fromString(url).map(Right(_)).getOrElse(Left(NonEmptyList.one(s"Invalid workflow reference: $url")))): Parse[CwlReference] |
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It seems like somewhere in all this abstraction we must be making an HTTP requests to actually get the url. How is it doing that?
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Eventually all this goes into a call to cwltool, which accepts commands in the form of cwltool --print-pre URL and gives us back an appropriate CWL string with any relative paths inside converted into fully-qualified references for us.
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Ah OK, I was hunting around in our Scala code for this but it makes total sense that we're handing it off
| commandResult.exitCode match { | ||
| case 0 => commandResult.out.string | ||
| case error => | ||
| throw new RuntimeException( | ||
| s"running CwlTool on file $file resulted in exit code $error and stderr ${commandResult.err.string}") | ||
| s"running CwlTool on file $reference resulted in exit code $error and stderr ${commandResult.err.string}") |
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ToL: Line 65 below uses ${reference.pathAsString} instead of $reference. Not sure if it matters anymore, but just noticed there was a difference.
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It does, and I've updated this.
reference.toString includes the "which tool/workflow in the file to look at" information, which is not relevant for a message about an unreadable file.
docs/developers/CwlParsing.md
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| The process of parsing CWL runs approximately like this: | ||
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| 1. Produce a canonical one-file representation of the CWL as a JSON object in memory | ||
| 1. Use Circe to turn that representation into scala case classes |
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docs/developers/CwlParsing.md
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| ## Convert the case classes into WOM representations | ||
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| As of today, CWL doesn't produce WOM bundles. Instead, it goes straight to executable. |
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cjllanwarne
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